Overview

When you publish manuscripts based on data generated at our facility, we would greatly appreciate an acknowledgement of our efforts. Please cite our facility as follows (for example):

Basic processing of the raw data were performed by the University of Illinois at Chicago Research Informatics Core (UICRIC).

We adhere to a general policy for acknowledgements and authorship as established by the Association for Biomolecular Resource Facilities (ABRF) , and we support the following statement from the ABRF.

The existence of core facilities depends in part on proper acknowledgment in publications. This is an important metric of the value of most core facilities. Proper acknowledgment of core facilities enables them to obtain financial and other support so that they may continue to provide their essential services in the best ways possible. It also helps core personnel to advance in their careers, adding to the overall health of the core facility.

Please contact us for assistance in drafting manuscripts.

Output Files

File Description Type
metagenomic_assembly.zip ZIP compressed FASTA file of all contigs in the assembly result
contig_counts.txt Raw read counts for assembled contigs result
orf_counts.txt Raw read counts for predicted ORFs result
contig_data.txt Details and normalized read counts (CPM) of the contigs result
contig_annotations.gff Gene annotations of predicted ORFs, as GFF file result
contig_annotations.txt Gene annotations of predicted ORFs, as TSV file result
annotation_results.zip ZIP file of annotation results as and GFF format with FASTA files of nucleotide and amino acid sequences for each ORF result
bins_data.txt Details the metagenomic bins result
Sample OriginalID
Sample_A Sample_A
Sample_B Sample_B
Sample_C Sample_C
Sample_D Sample_D
Sample_E Sample_E

Details

Method: cutadapt

Sequencing trimming using cutadapt

Custom Parameters
  • --report = minimal
  • -m = 70
  • --trim-n
  • --max-n = 1
  • -b = file:/mnt/store3/clustcrilab/reference/other/primers.fa
Method: Quality trimming

Quality trimming based on quality threshold and length parameters.

Custom Parameters
  • min length = 70
Method: Adapter trimming

Adapter/primer sequences were trimmed from the reads.

Custom Parameters
  • adapter = TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
  • adapter = GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
  • adapter = CAAGCAGAAGACGGCATACGAGAT
  • adapter = AATGATACGGCGACCACCGAGATCTACAC
  • adapter = AATGATACGGCGACCACCGAGATCTACACGTAAGGAGTCGTCGGCAGCGTC
  • adapter = CAGTTACGTATTGC
  • adapter = CGTTCTGTTTATGTTTCTTG
Method: Abiguous nucleotide trimming

Ambiguous nucleotides (N) were trimmed from the ends and reads with internal ambiguous nucleotides were discarded.

Custom Parameters
  • max-n = 1

Figure 1. Trimming results

Table 1. Trimming statistics Download table data

Sample Trim passed Ambig dropped Trim filter dropped Trim length dropped Percent passed Mean Length Mean Trimmed Length Quality trimmed bp
Sample_A 999622 368 0 10 99.96% 302.0 301.3 0
Sample_B 999600 396 0 4 99.96% 302.0 301.3 0
Sample_C 999608 384 0 8 99.96% 302.0 301.3 0
Sample_D 999634 339 0 27 99.96% 302.0 301.3 0
Sample_E 999630 354 0 16 99.96% 302.0 301.3 0

Details

Method: Ultra-fast and memory-efficient (meta-)genome assembler

MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

Figure 1. Coverage plot

Table 1. Assembly summaries by stage Download table data

Stage Count TotalLength Longest N50 N75 N90 L50 L75 L90
Raw assembly 134381 134935198 257627 1371 615 403 15636 54435 95285
Entropy filtered 25665 79102624 257627 4505 1799 1231 2955 10416 18505
Alignment filtered 25665 79102624 257627 4505 1799 1231 2955 10416 18505

Table 2. Basic contig statistics, all contigs Download table data

#ID length GC coverage S_2mer S_3mer S_4mer
k141_127182 257627 42.830 19.39 0.982 0.972 0.966
k141_51787 192195 46.638 21.83 0.994 0.990 0.987
k141_15909 154623 43.807 12.87 0.992 0.989 0.986
k141_132787 141456 43.165 17.90 0.984 0.974 0.968
k141_51970 140642 41.011 444.73 0.985 0.981 0.978
k141_124065 128929 43.880 15.42 0.983 0.973 0.966
k141_44847 124976 44.174 13.23 0.992 0.989 0.987
k141_3062 117795 42.627 12.52 0.989 0.986 0.983
k141_79811 117434 41.516 12.35 0.987 0.984 0.981
k141_64742 114374 45.247 12.77 0.987 0.976 0.969
k141_22725 111366 40.406 11.96 0.983 0.979 0.976
k141_20838 111288 42.586 14.69 0.981 0.971 0.964
k141_107469 109883 55.402 11.40 0.987 0.982 0.977
k141_76946 109634 43.705 21.25 0.979 0.970 0.964
k141_14199 108988 43.345 18.29 0.978 0.969 0.963
k141_72316 104440 43.103 16.49 0.982 0.971 0.964
k141_39487 102822 43.389 17.49 0.982 0.973 0.968
k141_127755 102231 43.178 20.53 0.981 0.973 0.968
k141_129443 101320 41.908 17.87 0.976 0.968 0.963
k141_121521 100942 42.808 11.99 0.989 0.985 0.982
k141_21619 99648 42.551 19.92 0.978 0.970 0.965
k141_94101 99116 44.053 20.65 0.982 0.974 0.969
k141_106849 97846 42.754 13.38 0.987 0.983 0.980
k141_69579 97297 40.252 18.80 0.981 0.975 0.972
k141_1006 95520 42.192 12.32 0.987 0.984 0.981
k141_85288 95074 45.237 21.98 0.993 0.990 0.986
k141_132600 95035 41.949 12.24 0.988 0.984 0.981
k141_1809 93768 44.553 11.25 0.992 0.989 0.985
k141_28491 92186 44.066 12.71 0.992 0.989 0.985
k141_24913 92043 44.668 23.04 0.990 0.987 0.984
k141_3849 90677 42.038 18.97 0.980 0.969 0.963
k141_89440 87489 43.002 19.47 0.980 0.972 0.967
k141_37188 87150 44.433 18.67 0.992 0.989 0.986
k141_94611 86511 41.783 21.92 0.974 0.965 0.960
k141_25196 83496 43.918 17.66 0.984 0.972 0.965
k141_124017 81881 40.760 19.21 0.982 0.973 0.966
k141_57003 79444 46.382 23.61 0.993 0.989 0.986
k141_59427 79433 42.713 18.67 0.985 0.976 0.970
k141_52326 79016 55.505 10.51 0.986 0.981 0.976
k141_73449 78916 43.014 20.21 0.977 0.968 0.962
k141_957 78906 44.861 16.41 0.986 0.975 0.968
k141_63155 78713 43.333 10.58 0.990 0.986 0.982
k141_2773 78359 41.596 24.09 0.984 0.980 0.978
k141_95630 76837 41.248 11.27 0.987 0.984 0.981
k141_12812 76749 39.266 17.68 0.977 0.970 0.965
k141_27717 76741 42.451 18.86 0.979 0.971 0.965
k141_16661 76507 46.249 22.65 0.993 0.990 0.987
k141_18855 76501 43.033 16.69 0.984 0.974 0.967
k141_91719 76230 41.166 18.18 0.975 0.967 0.962
k141_126790 75803 41.203 12.41 0.986 0.982 0.979
k141_68317 74672 44.539 16.68 0.987 0.976 0.969
k141_23154 74303 46.357 20.29 0.994 0.991 0.988
k141_122147 73821 47.908 23.23 0.996 0.992 0.989
k141_81107 72982 41.236 11.88 0.984 0.981 0.979
k141_98618 72649 57.274 12.47 0.983 0.977 0.973
k141_22257 71646 40.829 12.06 0.986 0.983 0.980
k141_75232 71589 43.177 22.94 0.987 0.984 0.981
k141_52461 71552 44.323 24.01 0.991 0.988 0.985
k141_113491 71338 43.562 11.40 0.991 0.987 0.984
k141_90654 71317 42.917 20.19 0.977 0.969 0.964
k141_78336 70751 43.725 11.40 0.992 0.988 0.984
k141_2006 70750 44.459 23.77 0.991 0.988 0.985
k141_86061 70285 44.490 24.58 0.990 0.987 0.984
k141_106531 70115 44.866 23.78 0.992 0.989 0.986
k141_76448 70085 41.283 22.11 0.985 0.983 0.981
k141_11394 68687 42.130 12.41 0.987 0.984 0.981
k141_86939 68657 45.888 20.02 0.991 0.987 0.984
k141_33252 68358 44.827 12.89 0.993 0.989 0.986
k141_26744 67456 57.563 6.68 0.986 0.981 0.977
k141_20627 66315 40.921 17.44 0.975 0.968 0.963
k141_85794 66204 44.686 24.23 0.992 0.989 0.986
k141_53141 65608 48.351 15.60 0.994 0.989 0.984
k141_38870 65564 46.564 24.32 0.993 0.989 0.986
k141_103525 65338 42.325 15.54 0.983 0.974 0.968
k141_109528 63964 44.677 12.30 0.993 0.990 0.986
k141_25206 63879 41.236 19.92 0.984 0.981 0.979
k141_30384 63089 56.311 12.04 0.987 0.982 0.978
k141_21085 62844 42.822 17.69 0.979 0.971 0.966
k141_107141 62712 37.902 22.27 0.972 0.966 0.961
k141_8110 61798 42.335 19.40 0.978 0.969 0.963
k141_82943 61465 42.120 12.73 0.981 0.977 0.973
k141_26853 59940 56.220 11.73 0.986 0.982 0.977
k141_119199 59016 56.341 11.65 0.985 0.978 0.973
k141_55548 58823 44.245 18.51 0.993 0.989 0.986
k141_35181 58347 40.940 13.04 0.976 0.968 0.963
k141_50008 58342 45.264 14.61 0.986 0.975 0.968
k141_88846 58131 45.086 12.93 0.993 0.990 0.986
k141_94779 57602 46.049 22.03 0.994 0.990 0.988
k141_2122 57403 43.834 17.17 0.986 0.975 0.968
k141_1585 57028 42.465 18.74 0.981 0.972 0.967
k141_4021 57018 38.525 17.74 0.976 0.971 0.967
k141_87913 55818 43.635 12.88 0.991 0.988 0.985
k141_42457 55594 45.377 20.85 0.992 0.989 0.985
k141_96850 55039 44.757 17.65 0.986 0.975 0.968
k141_11845 54911 44.303 13.69 0.985 0.975 0.968
k141_97665 54637 42.976 12.86 0.987 0.983 0.979
k141_102277 53765 41.774 19.06 0.971 0.962 0.956
k141_77313 53707 45.192 12.18 0.986 0.975 0.967
k141_1183 53472 42.306 20.51 0.978 0.972 0.967
k141_73924 53451 43.135 11.57 0.989 0.985 0.982
k141_77565 53268 41.768 11.79 0.985 0.981 0.978
k141_70888 52913 43.950 24.02 0.990 0.987 0.983
k141_61780 52729 46.299 21.60 0.992 0.988 0.983
k141_29816 52565 42.483 11.45 0.986 0.979 0.974
k141_118652 51575 40.159 17.82 0.971 0.963 0.959
k141_44207 51222 43.097 11.81 0.983 0.973 0.968
k141_64494 50907 46.481 23.04 0.993 0.990 0.986
k141_53777 50501 43.720 23.76 0.987 0.983 0.980
k141_132326 50489 56.280 11.52 0.984 0.979 0.974
k141_129718 50485 40.606 16.06 0.969 0.963 0.959
k141_122290 50291 43.809 12.72 0.992 0.988 0.985
k141_36755 50204 40.857 12.19 0.984 0.980 0.977
k141_92080 50001 42.101 17.04 0.976 0.969 0.964
k141_70340 49902 44.770 23.65 0.991 0.988 0.985
k141_643 49725 42.842 12.39 0.988 0.984 0.981
k141_102771 49579 45.116 21.61 0.991 0.988 0.985
k141_134067 49440 44.905 12.95 0.985 0.973 0.965
k141_118654 48564 42.789 11.89 0.989 0.985 0.982
k141_29269 48465 50.127 32.29 0.995 0.991 0.986
k141_44810 48326 57.961 14.58 0.980 0.972 0.966
k141_81735 48129 52.771 12.02 0.988 0.983 0.979
k141_39683 47905 40.198 11.97 0.977 0.968 0.963
k141_59464 47886 40.525 22.35 0.981 0.978 0.975
k141_115089 47433 40.535 11.66 0.978 0.974 0.971
k141_46140 47247 42.085 17.24 0.987 0.984 0.981
k141_45906 46876 44.782 15.32 0.984 0.973 0.965
k141_80039 46574 43.400 12.61 0.990 0.986 0.982
k141_60427 45934 44.588 22.01 0.991 0.987 0.984
k141_55220 45855 48.339 24.79 0.995 0.992 0.988
k141_99887 45847 41.455 11.40 0.984 0.981 0.977
k141_97605 45625 41.951 10.74 0.987 0.983 0.979
k141_91996 45537 44.136 21.00 0.987 0.983 0.980
k141_123056 44950 55.604 12.64 0.986 0.981 0.977
k141_59608 44912 44.485 17.34 0.977 0.971 0.965
k141_62200 44825 42.965 11.52 0.989 0.985 0.981
k141_42914 44692 44.411 10.81 0.993 0.989 0.986
k141_109757 44649 45.782 12.00 0.995 0.990 0.986
k141_70564 44344 43.695 11.34 0.992 0.989 0.985
k141_51942 44274 42.343 14.13 0.983 0.980 0.976
k141_88787 44018 45.856 23.12 0.992 0.988 0.985
k141_76289 43949 39.762 12.22 0.982 0.979 0.977
k141_1581 43923 44.514 13.15 0.993 0.989 0.986
k141_80954 43896 39.922 17.82 0.981 0.979 0.976
k141_2138 43783 41.185 16.58 0.981 0.976 0.970
k141_130745 43726 54.247 10.86 0.988 0.983 0.979
k141_52015 43554 45.252 24.06 0.990 0.987 0.983
k141_55780 43195 53.555 14.53 0.990 0.984 0.980
k141_57158 43021 46.405 24.13 0.993 0.989 0.986
k141_89506 42990 49.039 15.99 0.994 0.990 0.984
k141_131668 42829 46.212 21.79 0.993 0.989 0.985
k141_87545 42753 41.555 11.79 0.986 0.982 0.979
k141_92461 42577 54.762 10.03 0.987 0.980 0.975
k141_31844 42482 41.208 10.69 0.985 0.982 0.978
k141_115808 42452 53.124 10.49 0.990 0.985 0.981
k141_118409 42256 56.939 12.17 0.986 0.981 0.976
k141_92504 41890 46.744 23.21 0.993 0.989 0.986
k141_68464 41609 46.406 21.12 0.992 0.988 0.984
k141_45270 41577 41.497 21.56 0.975 0.967 0.962
k141_53156 41539 42.664 13.88 0.982 0.972 0.965
k141_124806 41472 45.161 12.90 0.994 0.991 0.987
k141_84227 41091 45.051 12.17 0.984 0.974 0.966
k141_102507 41060 44.576 12.82 0.987 0.979 0.972
k141_106022 40985 41.000 10.65 0.978 0.969 0.964
k141_52747 40830 44.159 11.63 0.985 0.973 0.965
k141_131812 40759 45.803 20.50 0.993 0.989 0.985
k141_30181 40596 42.364 11.43 0.987 0.984 0.981
k141_100564 40451 44.427 15.46 0.985 0.974 0.966
k141_31829 40004 44.568 13.00 0.991 0.987 0.984
k141_25018 39991 43.195 12.68 0.989 0.986 0.983
k141_18496 39974 44.284 22.99 0.990 0.987 0.984
k141_40098 39951 39.416 13.10 0.973 0.967 0.963
k141_32527 39873 44.408 22.51 0.992 0.989 0.986
k141_34686 39186 45.534 11.96 0.988 0.979 0.972
k141_92267 39081 43.975 12.73 0.984 0.973 0.965
k141_105791 38956 40.818 15.32 0.979 0.975 0.972
k141_125536 38931 38.733 11.49 0.975 0.972 0.969
k141_125757 38856 42.132 13.74 0.973 0.965 0.959
k141_120379 38810 56.501 12.36 0.984 0.979 0.974
k141_131428 38726 43.242 14.89 0.983 0.975 0.969
k141_119061 38586 44.801 21.46 0.992 0.989 0.985
k141_21473 38411 46.711 12.17 0.994 0.990 0.986
k141_112341 38105 55.037 11.14 0.986 0.981 0.977
k141_111097 37758 45.755 23.99 0.992 0.988 0.985
k141_105176 37422 55.652 14.35 0.984 0.976 0.969
k141_1796 37318 43.470 12.83 0.979 0.970 0.964
k141_76431 37146 50.046 9.90 0.990 0.985 0.981
k141_3267 37039 42.525 12.00 0.989 0.985 0.982
k141_104561 37033 44.325 12.75 0.993 0.989 0.985
k141_24343 36679 41.498 11.80 0.986 0.983 0.980
k141_45088 36622 56.087 11.20 0.986 0.980 0.976
k141_123013 36215 42.540 11.85 0.989 0.985 0.982
k141_135120 36178 45.077 21.51 0.990 0.986 0.983
k141_121915 36015 53.117 12.49 0.991 0.987 0.983
k141_76193 35815 42.477 11.23 0.987 0.984 0.980
k141_58174 35731 39.727 15.28 0.974 0.967 0.963
k141_105902 35577 41.996 13.12 0.987 0.984 0.981
k141_12702 35438 44.035 13.49 0.990 0.987 0.983
k141_3964 35394 40.815 13.30 0.986 0.982 0.978
k141_22747 35321 41.562 11.52 0.985 0.982 0.978
k141_83355 35165 45.005 22.64 0.991 0.987 0.984
k141_9814 35082 52.531 13.88 0.994 0.989 0.984
k141_51944 34915 52.860 20.69 0.992 0.988 0.984
k141_29371 34711 42.929 11.33 0.990 0.986 0.983
k141_30705 34704 43.205 16.91 0.984 0.973 0.966
k141_45366 34261 43.151 20.17 0.989 0.986 0.983
k141_57048 34224 43.396 20.34 0.977 0.967 0.961
k141_99960 34085 45.193 11.99 0.986 0.975 0.967
k141_59620 34069 45.064 22.31 0.990 0.986 0.983
k141_17502 33687 49.120 20.05 0.996 0.993 0.989
k141_94843 33575 42.508 19.77 0.977 0.968 0.961
k141_46834 33079 50.521 10.07 0.993 0.985 0.979
k141_134328 32978 52.371 9.79 0.995 0.991 0.986
k141_64124 32785 42.022 14.88 0.989 0.987 0.985
k141_118666 32678 52.696 9.70 0.991 0.985 0.979
k141_75277 32674 44.375 12.27 0.992 0.988 0.985
k141_117132 32526 45.367 22.27 0.992 0.989 0.986
k141_47136 32380 44.074 11.62 0.991 0.987 0.983
k141_95599 32346 40.765 18.06 0.970 0.961 0.954
k141_117628 32226 41.578 11.80 0.986 0.983 0.980
k141_70903 32166 55.198 12.18 0.986 0.981 0.976
k141_68260 31859 43.178 11.14 0.989 0.986 0.982
k141_20213 31763 43.012 12.00 0.989 0.981 0.976
k141_52130 31699 40.377 9.74 0.976 0.969 0.965
k141_110256 31667 42.072 11.19 0.988 0.985 0.982
k141_130210 31631 57.712 12.92 0.981 0.976 0.971
k141_20610 31525 44.019 21.26 0.987 0.983 0.980
k141_85153 31462 58.547 14.05 0.979 0.971 0.964
k141_2227 31416 57.668 13.87 0.982 0.975 0.968
k141_71521 31239 51.887 10.82 0.992 0.988 0.984
k141_19158 31050 37.871 53.44 0.973 0.969 0.965
k141_108130 31046 51.079 31.60 0.994 0.990 0.986
k141_61873 31037 55.389 12.04 0.988 0.981 0.974
k141_91169 31020 39.936 17.36 0.968 0.960 0.955
k141_82135 30966 40.018 13.00 0.973 0.965 0.959
k141_85899 30912 41.418 28.03 0.985 0.982 0.979
k141_41364 30752 43.714 21.76 0.983 0.977 0.972
k141_71785 30583 57.980 13.01 0.981 0.975 0.970
k141_33487 30567 42.716 12.57 0.979 0.970 0.964
k141_83704 30437 59.546 11.61 0.976 0.969 0.962
k141_132950 30268 42.077 17.94 0.983 0.974 0.968
k141_19240 30216 47.012 23.62 0.991 0.986 0.982
k141_126532 30160 51.273 11.32 0.994 0.990 0.986
k141_40284 30133 46.836 21.86 0.993 0.989 0.985
k141_15650 30037 59.587 12.34 0.973 0.965 0.959
k141_103912 29924 44.359 21.57 0.991 0.987 0.984
k141_102639 29912 44.267 22.02 0.988 0.984 0.981
k141_103942 29900 43.702 11.93 0.984 0.971 0.963
k141_98769 29760 44.681 24.05 0.989 0.986 0.982
k141_68815 29747 42.562 10.48 0.981 0.971 0.964
k141_28224 29739 39.362 11.43 0.977 0.974 0.972
k141_22756 29694 42.386 11.23 0.982 0.972 0.965
k141_46760 29580 54.547 11.00 0.991 0.985 0.980
k141_92312 29570 43.612 12.77 0.990 0.987 0.983
k141_63166 29570 45.036 13.93 0.985 0.975 0.968
k141_61599 29493 57.180 11.01 0.984 0.976 0.969
k141_131754 29457 44.078 10.58 0.991 0.987 0.982
k141_85673 29372 44.879 11.35 0.993 0.989 0.986
k141_103582 29337 34.577 10.40 0.956 0.954 0.952
k141_120720 29217 43.937 10.45 0.991 0.986 0.982
k141_88543 29144 43.120 20.63 0.983 0.979 0.976
k141_69511 29130 56.399 11.00 0.984 0.975 0.967
k141_33891 29061 40.759 11.74 0.985 0.982 0.979
k141_111519 29004 46.073 12.91 0.988 0.975 0.965
k141_35032 28913 46.443 51.08 0.989 0.981 0.975
k141_44529 28846 50.257 9.93 0.995 0.989 0.984
k141_119215 28748 38.250 10.33 0.974 0.971 0.968
k141_128322 28717 56.016 12.95 0.988 0.984 0.979
k141_8647 28644 49.902 9.71 0.992 0.985 0.979
k141_54079 28616 39.908 17.47 0.976 0.970 0.966
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k141_89635 3063 47.307 7.29 0.990 0.984 0.973
k141_58034 3062 44.219 6.56 0.988 0.981 0.970
k141_47917 3062 50.294 6.22 0.997 0.991 0.981
k141_17395 3062 42.293 6.47 0.983 0.978 0.968
k141_11610 3062 36.675 6.63 0.971 0.967 0.959
k141_28890 3061 50.180 8.20 0.990 0.980 0.969
k141_117259 3061 34.956 5.98 0.961 0.956 0.949
k141_53337 3060 54.183 13.17 0.986 0.979 0.966
k141_1383 3060 54.542 14.47 0.991 0.983 0.972
k141_113809 3060 51.275 7.81 0.995 0.984 0.973
k141_54350 3059 46.715 6.85 0.992 0.985 0.975
k141_112020 3058 40.320 6.75 0.972 0.962 0.948
k141_5830 3057 41.315 7.36 0.977 0.972 0.963
k141_102837 3057 58.194 7.55 0.983 0.971 0.957
k141_53327 3056 38.743 11.84 0.971 0.964 0.952
k141_40618 3056 49.215 5.17 0.992 0.982 0.971
k141_104412 3056 62.173 9.31 0.971 0.961 0.949
k141_67023 3054 40.046 9.28 0.967 0.956 0.945
k141_42350 3054 48.527 11.67 0.995 0.987 0.977
k141_55903 3053 46.544 7.53 0.988 0.981 0.972
k141_50526 3053 50.147 7.35 0.987 0.978 0.968
k141_39400 3053 47.625 12.80 0.996 0.990 0.981
k141_112004 3052 47.543 5.74 0.984 0.970 0.957
k141_85426 3051 46.345 14.31 0.991 0.988 0.981
k141_112197 3051 51.754 7.17 0.984 0.975 0.963
k141_110405 3051 41.921 6.71 0.978 0.968 0.958
k141_34789 3050 37.934 10.65 0.974 0.969 0.960
k141_135083 3050 62.984 8.12 0.963 0.950 0.936
k141_118667 3050 48.000 5.01 0.987 0.976 0.964
k141_47456 3049 40.177 6.18 0.975 0.969 0.960
k141_44569 3049 48.639 9.85 0.993 0.983 0.974
k141_29185 3049 38.373 7.23 0.974 0.969 0.960
k141_125486 3049 42.703 7.97 0.987 0.980 0.971
k141_130127 3047 53.167 5.66 0.982 0.971 0.959
k141_89392 3046 32.797 5.33 0.950 0.946 0.939
k141_131806 3046 36.376 11.82 0.952 0.948 0.940
k141_50126 3045 40.755 9.08 0.972 0.965 0.953
k141_128285 3045 56.913 7.20 0.985 0.976 0.963
k141_79739 3044 47.536 5.89 0.993 0.986 0.975
k141_55305 3044 50.821 6.35 0.990 0.984 0.974
k141_24359 3044 60.480 5.77 0.977 0.968 0.957
k141_11239 3044 47.043 9.16 0.991 0.983 0.972
k141_85195 3043 42.754 8.75 0.987 0.978 0.968
k141_24160 3042 43.886 7.40 0.976 0.968 0.957
k141_132082 3042 40.204 10.67 0.980 0.975 0.967
k141_25242 3041 48.504 4.80 0.991 0.978 0.965
k141_124352 3041 57.284 8.16 0.972 0.960 0.947
k141_93943 3040 28.651 4.75 0.919 0.915 0.909
k141_76785 3040 38.882 12.44 0.977 0.970 0.959
k141_40141 3039 35.176 6.95 0.960 0.956 0.948
k141_132511 3039 36.624 6.52 0.964 0.961 0.953
k141_92376 3038 44.141 8.35 0.979 0.971 0.962
k141_131839 3038 46.708 5.54 0.990 0.978 0.966
Displaying first 5000 of 134382 lines

Table 3. Basic contig statistics, filtered contigs Download table data

#ID length GC coverage S_2mer S_3mer S_4mer
k141_127182 257627 42.830 19.39 0.982 0.972 0.966
k141_51787 192195 46.638 21.83 0.994 0.990 0.987
k141_15909 154623 43.807 12.87 0.992 0.989 0.986
k141_132787 141456 43.165 17.90 0.984 0.974 0.968
k141_51970 140642 41.011 444.73 0.985 0.981 0.978
k141_124065 128929 43.880 15.42 0.983 0.973 0.966
k141_44847 124976 44.174 13.23 0.992 0.989 0.987
k141_3062 117795 42.627 12.52 0.989 0.986 0.983
k141_79811 117434 41.516 12.35 0.987 0.984 0.981
k141_64742 114374 45.247 12.77 0.987 0.976 0.969
k141_22725 111366 40.406 11.96 0.983 0.979 0.976
k141_20838 111288 42.586 14.69 0.981 0.971 0.964
k141_107469 109883 55.402 11.40 0.987 0.982 0.977
k141_76946 109634 43.705 21.25 0.979 0.970 0.964
k141_14199 108988 43.345 18.29 0.978 0.969 0.963
k141_72316 104440 43.103 16.49 0.982 0.971 0.964
k141_39487 102822 43.389 17.49 0.982 0.973 0.968
k141_127755 102231 43.178 20.53 0.981 0.973 0.968
k141_129443 101320 41.908 17.87 0.976 0.968 0.963
k141_121521 100942 42.808 11.99 0.989 0.985 0.982
k141_21619 99648 42.551 19.92 0.978 0.970 0.965
k141_94101 99116 44.053 20.65 0.982 0.974 0.969
k141_106849 97846 42.754 13.38 0.987 0.983 0.980
k141_69579 97297 40.252 18.80 0.981 0.975 0.972
k141_1006 95520 42.192 12.32 0.987 0.984 0.981
k141_85288 95074 45.237 21.98 0.993 0.990 0.986
k141_132600 95035 41.949 12.24 0.988 0.984 0.981
k141_1809 93768 44.553 11.25 0.992 0.989 0.985
k141_28491 92186 44.066 12.71 0.992 0.989 0.985
k141_24913 92043 44.668 23.04 0.990 0.987 0.984
k141_3849 90677 42.038 18.97 0.980 0.969 0.963
k141_89440 87489 43.002 19.47 0.980 0.972 0.967
k141_37188 87150 44.433 18.67 0.992 0.989 0.986
k141_94611 86511 41.783 21.92 0.974 0.965 0.960
k141_25196 83496 43.918 17.66 0.984 0.972 0.965
k141_124017 81881 40.760 19.21 0.982 0.973 0.966
k141_57003 79444 46.382 23.61 0.993 0.989 0.986
k141_59427 79433 42.713 18.67 0.985 0.976 0.970
k141_52326 79016 55.505 10.51 0.986 0.981 0.976
k141_73449 78916 43.014 20.21 0.977 0.968 0.962
k141_957 78906 44.861 16.41 0.986 0.975 0.968
k141_63155 78713 43.333 10.58 0.990 0.986 0.982
k141_2773 78359 41.596 24.09 0.984 0.980 0.978
k141_95630 76837 41.248 11.27 0.987 0.984 0.981
k141_12812 76749 39.266 17.68 0.977 0.970 0.965
k141_27717 76741 42.451 18.86 0.979 0.971 0.965
k141_16661 76507 46.249 22.65 0.993 0.990 0.987
k141_18855 76501 43.033 16.69 0.984 0.974 0.967
k141_91719 76230 41.166 18.18 0.975 0.967 0.962
k141_126790 75803 41.203 12.41 0.986 0.982 0.979
k141_68317 74672 44.539 16.68 0.987 0.976 0.969
k141_23154 74303 46.357 20.29 0.994 0.991 0.988
k141_122147 73821 47.908 23.23 0.996 0.992 0.989
k141_81107 72982 41.236 11.88 0.984 0.981 0.979
k141_98618 72649 57.274 12.47 0.983 0.977 0.973
k141_22257 71646 40.829 12.06 0.986 0.983 0.980
k141_75232 71589 43.177 22.94 0.987 0.984 0.981
k141_52461 71552 44.323 24.01 0.991 0.988 0.985
k141_113491 71338 43.562 11.40 0.991 0.987 0.984
k141_90654 71317 42.917 20.19 0.977 0.969 0.964
k141_78336 70751 43.725 11.40 0.992 0.988 0.984
k141_2006 70750 44.459 23.77 0.991 0.988 0.985
k141_86061 70285 44.490 24.58 0.990 0.987 0.984
k141_106531 70115 44.866 23.78 0.992 0.989 0.986
k141_76448 70085 41.283 22.11 0.985 0.983 0.981
k141_11394 68687 42.130 12.41 0.987 0.984 0.981
k141_86939 68657 45.888 20.02 0.991 0.987 0.984
k141_33252 68358 44.827 12.89 0.993 0.989 0.986
k141_26744 67456 57.563 6.68 0.986 0.981 0.977
k141_20627 66315 40.921 17.44 0.975 0.968 0.963
k141_85794 66204 44.686 24.23 0.992 0.989 0.986
k141_53141 65608 48.351 15.60 0.994 0.989 0.984
k141_38870 65564 46.564 24.32 0.993 0.989 0.986
k141_103525 65338 42.325 15.54 0.983 0.974 0.968
k141_109528 63964 44.677 12.30 0.993 0.990 0.986
k141_25206 63879 41.236 19.92 0.984 0.981 0.979
k141_30384 63089 56.311 12.04 0.987 0.982 0.978
k141_21085 62844 42.822 17.69 0.979 0.971 0.966
k141_107141 62712 37.902 22.27 0.972 0.966 0.961
k141_8110 61798 42.335 19.40 0.978 0.969 0.963
k141_82943 61465 42.120 12.73 0.981 0.977 0.973
k141_26853 59940 56.220 11.73 0.986 0.982 0.977
k141_119199 59016 56.341 11.65 0.985 0.978 0.973
k141_55548 58823 44.245 18.51 0.993 0.989 0.986
k141_35181 58347 40.940 13.04 0.976 0.968 0.963
k141_50008 58342 45.264 14.61 0.986 0.975 0.968
k141_88846 58131 45.086 12.93 0.993 0.990 0.986
k141_94779 57602 46.049 22.03 0.994 0.990 0.988
k141_2122 57403 43.834 17.17 0.986 0.975 0.968
k141_1585 57028 42.465 18.74 0.981 0.972 0.967
k141_4021 57018 38.525 17.74 0.976 0.971 0.967
k141_87913 55818 43.635 12.88 0.991 0.988 0.985
k141_42457 55594 45.377 20.85 0.992 0.989 0.985
k141_96850 55039 44.757 17.65 0.986 0.975 0.968
k141_11845 54911 44.303 13.69 0.985 0.975 0.968
k141_97665 54637 42.976 12.86 0.987 0.983 0.979
k141_102277 53765 41.774 19.06 0.971 0.962 0.956
k141_77313 53707 45.192 12.18 0.986 0.975 0.967
k141_1183 53472 42.306 20.51 0.978 0.972 0.967
k141_73924 53451 43.135 11.57 0.989 0.985 0.982
k141_77565 53268 41.768 11.79 0.985 0.981 0.978
k141_70888 52913 43.950 24.02 0.990 0.987 0.983
k141_61780 52729 46.299 21.60 0.992 0.988 0.983
k141_29816 52565 42.483 11.45 0.986 0.979 0.974
k141_118652 51575 40.159 17.82 0.971 0.963 0.959
k141_44207 51222 43.097 11.81 0.983 0.973 0.968
k141_64494 50907 46.481 23.04 0.993 0.990 0.986
k141_53777 50501 43.720 23.76 0.987 0.983 0.980
k141_132326 50489 56.280 11.52 0.984 0.979 0.974
k141_129718 50485 40.606 16.06 0.969 0.963 0.959
k141_122290 50291 43.809 12.72 0.992 0.988 0.985
k141_36755 50204 40.857 12.19 0.984 0.980 0.977
k141_92080 50001 42.101 17.04 0.976 0.969 0.964
k141_70340 49902 44.770 23.65 0.991 0.988 0.985
k141_643 49725 42.842 12.39 0.988 0.984 0.981
k141_102771 49579 45.116 21.61 0.991 0.988 0.985
k141_134067 49440 44.905 12.95 0.985 0.973 0.965
k141_118654 48564 42.789 11.89 0.989 0.985 0.982
k141_29269 48465 50.127 32.29 0.995 0.991 0.986
k141_44810 48326 57.961 14.58 0.980 0.972 0.966
k141_81735 48129 52.771 12.02 0.988 0.983 0.979
k141_39683 47905 40.198 11.97 0.977 0.968 0.963
k141_59464 47886 40.525 22.35 0.981 0.978 0.975
k141_115089 47433 40.535 11.66 0.978 0.974 0.971
k141_46140 47247 42.085 17.24 0.987 0.984 0.981
k141_45906 46876 44.782 15.32 0.984 0.973 0.965
k141_80039 46574 43.400 12.61 0.990 0.986 0.982
k141_60427 45934 44.588 22.01 0.991 0.987 0.984
k141_55220 45855 48.339 24.79 0.995 0.992 0.988
k141_99887 45847 41.455 11.40 0.984 0.981 0.977
k141_97605 45625 41.951 10.74 0.987 0.983 0.979
k141_91996 45537 44.136 21.00 0.987 0.983 0.980
k141_123056 44950 55.604 12.64 0.986 0.981 0.977
k141_59608 44912 44.485 17.34 0.977 0.971 0.965
k141_62200 44825 42.965 11.52 0.989 0.985 0.981
k141_42914 44692 44.411 10.81 0.993 0.989 0.986
k141_109757 44649 45.782 12.00 0.995 0.990 0.986
k141_70564 44344 43.695 11.34 0.992 0.989 0.985
k141_51942 44274 42.343 14.13 0.983 0.980 0.976
k141_88787 44018 45.856 23.12 0.992 0.988 0.985
k141_76289 43949 39.762 12.22 0.982 0.979 0.977
k141_1581 43923 44.514 13.15 0.993 0.989 0.986
k141_80954 43896 39.922 17.82 0.981 0.979 0.976
k141_2138 43783 41.185 16.58 0.981 0.976 0.970
k141_130745 43726 54.247 10.86 0.988 0.983 0.979
k141_52015 43554 45.252 24.06 0.990 0.987 0.983
k141_55780 43195 53.555 14.53 0.990 0.984 0.980
k141_57158 43021 46.405 24.13 0.993 0.989 0.986
k141_89506 42990 49.039 15.99 0.994 0.990 0.984
k141_131668 42829 46.212 21.79 0.993 0.989 0.985
k141_87545 42753 41.555 11.79 0.986 0.982 0.979
k141_92461 42577 54.762 10.03 0.987 0.980 0.975
k141_31844 42482 41.208 10.69 0.985 0.982 0.978
k141_115808 42452 53.124 10.49 0.990 0.985 0.981
k141_118409 42256 56.939 12.17 0.986 0.981 0.976
k141_92504 41890 46.744 23.21 0.993 0.989 0.986
k141_68464 41609 46.406 21.12 0.992 0.988 0.984
k141_45270 41577 41.497 21.56 0.975 0.967 0.962
k141_53156 41539 42.664 13.88 0.982 0.972 0.965
k141_124806 41472 45.161 12.90 0.994 0.991 0.987
k141_84227 41091 45.051 12.17 0.984 0.974 0.966
k141_102507 41060 44.576 12.82 0.987 0.979 0.972
k141_106022 40985 41.000 10.65 0.978 0.969 0.964
k141_52747 40830 44.159 11.63 0.985 0.973 0.965
k141_131812 40759 45.803 20.50 0.993 0.989 0.985
k141_30181 40596 42.364 11.43 0.987 0.984 0.981
k141_100564 40451 44.427 15.46 0.985 0.974 0.966
k141_31829 40004 44.568 13.00 0.991 0.987 0.984
k141_25018 39991 43.195 12.68 0.989 0.986 0.983
k141_18496 39974 44.284 22.99 0.990 0.987 0.984
k141_40098 39951 39.416 13.10 0.973 0.967 0.963
k141_32527 39873 44.408 22.51 0.992 0.989 0.986
k141_34686 39186 45.534 11.96 0.988 0.979 0.972
k141_92267 39081 43.975 12.73 0.984 0.973 0.965
k141_105791 38956 40.818 15.32 0.979 0.975 0.972
k141_125536 38931 38.733 11.49 0.975 0.972 0.969
k141_125757 38856 42.132 13.74 0.973 0.965 0.959
k141_120379 38810 56.501 12.36 0.984 0.979 0.974
k141_131428 38726 43.242 14.89 0.983 0.975 0.969
k141_119061 38586 44.801 21.46 0.992 0.989 0.985
k141_21473 38411 46.711 12.17 0.994 0.990 0.986
k141_112341 38105 55.037 11.14 0.986 0.981 0.977
k141_111097 37758 45.755 23.99 0.992 0.988 0.985
k141_105176 37422 55.652 14.35 0.984 0.976 0.969
k141_1796 37318 43.470 12.83 0.979 0.970 0.964
k141_76431 37146 50.046 9.90 0.990 0.985 0.981
k141_3267 37039 42.525 12.00 0.989 0.985 0.982
k141_104561 37033 44.325 12.75 0.993 0.989 0.985
k141_24343 36679 41.498 11.80 0.986 0.983 0.980
k141_45088 36622 56.087 11.20 0.986 0.980 0.976
k141_123013 36215 42.540 11.85 0.989 0.985 0.982
k141_135120 36178 45.077 21.51 0.990 0.986 0.983
k141_121915 36015 53.117 12.49 0.991 0.987 0.983
k141_76193 35815 42.477 11.23 0.987 0.984 0.980
k141_58174 35731 39.727 15.28 0.974 0.967 0.963
k141_105902 35577 41.996 13.12 0.987 0.984 0.981
k141_12702 35438 44.035 13.49 0.990 0.987 0.983
k141_3964 35394 40.815 13.30 0.986 0.982 0.978
k141_22747 35321 41.562 11.52 0.985 0.982 0.978
k141_83355 35165 45.005 22.64 0.991 0.987 0.984
k141_9814 35082 52.531 13.88 0.994 0.989 0.984
k141_51944 34915 52.860 20.69 0.992 0.988 0.984
k141_29371 34711 42.929 11.33 0.990 0.986 0.983
k141_30705 34704 43.205 16.91 0.984 0.973 0.966
k141_45366 34261 43.151 20.17 0.989 0.986 0.983
k141_57048 34224 43.396 20.34 0.977 0.967 0.961
k141_99960 34085 45.193 11.99 0.986 0.975 0.967
k141_59620 34069 45.064 22.31 0.990 0.986 0.983
k141_17502 33687 49.120 20.05 0.996 0.993 0.989
k141_94843 33575 42.508 19.77 0.977 0.968 0.961
k141_46834 33079 50.521 10.07 0.993 0.985 0.979
k141_134328 32978 52.371 9.79 0.995 0.991 0.986
k141_64124 32785 42.022 14.88 0.989 0.987 0.985
k141_118666 32678 52.696 9.70 0.991 0.985 0.979
k141_75277 32674 44.375 12.27 0.992 0.988 0.985
k141_117132 32526 45.367 22.27 0.992 0.989 0.986
k141_47136 32380 44.074 11.62 0.991 0.987 0.983
k141_95599 32346 40.765 18.06 0.970 0.961 0.954
k141_117628 32226 41.578 11.80 0.986 0.983 0.980
k141_70903 32166 55.198 12.18 0.986 0.981 0.976
k141_68260 31859 43.178 11.14 0.989 0.986 0.982
k141_20213 31763 43.012 12.00 0.989 0.981 0.976
k141_52130 31699 40.377 9.74 0.976 0.969 0.965
k141_110256 31667 42.072 11.19 0.988 0.985 0.982
k141_130210 31631 57.712 12.92 0.981 0.976 0.971
k141_20610 31525 44.019 21.26 0.987 0.983 0.980
k141_85153 31462 58.547 14.05 0.979 0.971 0.964
k141_2227 31416 57.668 13.87 0.982 0.975 0.968
k141_71521 31239 51.887 10.82 0.992 0.988 0.984
k141_19158 31050 37.871 53.44 0.973 0.969 0.965
k141_108130 31046 51.079 31.60 0.994 0.990 0.986
k141_61873 31037 55.389 12.04 0.988 0.981 0.974
k141_91169 31020 39.936 17.36 0.968 0.960 0.955
k141_82135 30966 40.018 13.00 0.973 0.965 0.959
k141_85899 30912 41.418 28.03 0.985 0.982 0.979
k141_41364 30752 43.714 21.76 0.983 0.977 0.972
k141_71785 30583 57.980 13.01 0.981 0.975 0.970
k141_33487 30567 42.716 12.57 0.979 0.970 0.964
k141_83704 30437 59.546 11.61 0.976 0.969 0.962
k141_132950 30268 42.077 17.94 0.983 0.974 0.968
k141_19240 30216 47.012 23.62 0.991 0.986 0.982
k141_126532 30160 51.273 11.32 0.994 0.990 0.986
k141_40284 30133 46.836 21.86 0.993 0.989 0.985
k141_15650 30037 59.587 12.34 0.973 0.965 0.959
k141_103912 29924 44.359 21.57 0.991 0.987 0.984
k141_102639 29912 44.267 22.02 0.988 0.984 0.981
k141_103942 29900 43.702 11.93 0.984 0.971 0.963
k141_98769 29760 44.681 24.05 0.989 0.986 0.982
k141_68815 29747 42.562 10.48 0.981 0.971 0.964
k141_28224 29739 39.362 11.43 0.977 0.974 0.972
k141_22756 29694 42.386 11.23 0.982 0.972 0.965
k141_46760 29580 54.547 11.00 0.991 0.985 0.980
k141_92312 29570 43.612 12.77 0.990 0.987 0.983
k141_63166 29570 45.036 13.93 0.985 0.975 0.968
k141_61599 29493 57.180 11.01 0.984 0.976 0.969
k141_131754 29457 44.078 10.58 0.991 0.987 0.982
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k141_46348 3068 53.553 6.59 0.992 0.985 0.974
k141_21733 3068 44.654 7.87 0.988 0.980 0.970
k141_24382 3067 50.342 7.73 0.987 0.973 0.960
k141_120139 3067 44.799 11.05 0.989 0.983 0.975
k141_76094 3066 42.009 9.41 0.988 0.981 0.973
k141_25145 3066 56.654 11.53 0.984 0.973 0.961
k141_2038 3066 39.824 11.18 0.978 0.972 0.962
k141_123237 3065 47.308 8.43 0.985 0.974 0.963
k141_79187 3064 46.475 6.18 0.985 0.975 0.964
k141_77777 3064 42.591 14.51 0.981 0.971 0.960
k141_89635 3063 47.307 7.29 0.990 0.984 0.973
k141_58034 3062 44.219 6.56 0.988 0.981 0.970
k141_47917 3062 50.294 6.22 0.997 0.991 0.981
k141_17395 3062 42.293 6.47 0.983 0.978 0.968
k141_11610 3062 36.675 6.63 0.971 0.967 0.959
k141_28890 3061 50.180 8.20 0.990 0.980 0.969
k141_117259 3061 34.956 5.98 0.961 0.956 0.949
k141_53337 3060 54.183 13.17 0.986 0.979 0.966
k141_1383 3060 54.542 14.47 0.991 0.983 0.972
k141_113809 3060 51.275 7.81 0.995 0.984 0.973
k141_54350 3059 46.715 6.85 0.992 0.985 0.975
k141_112020 3058 40.320 6.75 0.972 0.962 0.948
k141_5830 3057 41.315 7.36 0.977 0.972 0.963
k141_102837 3057 58.194 7.55 0.983 0.971 0.957
k141_53327 3056 38.743 11.84 0.971 0.964 0.952
k141_40618 3056 49.215 5.17 0.992 0.982 0.971
k141_104412 3056 62.173 9.31 0.971 0.961 0.949
k141_67023 3054 40.046 9.28 0.967 0.956 0.945
k141_42350 3054 48.527 11.67 0.995 0.987 0.977
k141_55903 3053 46.544 7.53 0.988 0.981 0.972
k141_50526 3053 50.147 7.35 0.987 0.978 0.968
k141_39400 3053 47.625 12.80 0.996 0.990 0.981
k141_112004 3052 47.543 5.74 0.984 0.970 0.957
k141_85426 3051 46.345 14.31 0.991 0.988 0.981
k141_112197 3051 51.754 7.17 0.984 0.975 0.963
k141_110405 3051 41.921 6.71 0.978 0.968 0.958
k141_34789 3050 37.934 10.65 0.974 0.969 0.960
k141_135083 3050 62.984 8.12 0.963 0.950 0.936
k141_118667 3050 48.000 5.01 0.987 0.976 0.964
k141_47456 3049 40.177 6.18 0.975 0.969 0.960
k141_44569 3049 48.639 9.85 0.993 0.983 0.974
k141_29185 3049 38.373 7.23 0.974 0.969 0.960
k141_125486 3049 42.703 7.97 0.987 0.980 0.971
k141_130127 3047 53.167 5.66 0.982 0.971 0.959
k141_89392 3046 32.797 5.33 0.950 0.946 0.939
k141_131806 3046 36.376 11.82 0.952 0.948 0.940
k141_50126 3045 40.755 9.08 0.972 0.965 0.953
k141_128285 3045 56.913 7.20 0.985 0.976 0.963
k141_79739 3044 47.536 5.89 0.993 0.986 0.975
k141_55305 3044 50.821 6.35 0.990 0.984 0.974
k141_24359 3044 60.480 5.77 0.977 0.968 0.957
k141_11239 3044 47.043 9.16 0.991 0.983 0.972
k141_85195 3043 42.754 8.75 0.987 0.978 0.968
k141_24160 3042 43.886 7.40 0.976 0.968 0.957
k141_132082 3042 40.204 10.67 0.980 0.975 0.967
k141_25242 3041 48.504 4.80 0.991 0.978 0.965
k141_124352 3041 57.284 8.16 0.972 0.960 0.947
k141_93943 3040 28.651 4.75 0.919 0.915 0.909
k141_76785 3040 38.882 12.44 0.977 0.970 0.959
k141_40141 3039 35.176 6.95 0.960 0.956 0.948
k141_132511 3039 36.624 6.52 0.964 0.961 0.953
k141_92376 3038 44.141 8.35 0.979 0.971 0.962
k141_131839 3038 46.708 5.54 0.990 0.978 0.966
Displaying first 5000 of 134382 lines

Details

Method: eggNOG Mapper

Fast genome-wide functional annotation through orthology assignment.

Custom Parameters
  • --itype = metagenome
  • --genepred = prodigal
  • --decorate_gff = yes
Method: Bacterial ribosomal RNA predictor

Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), metazoan mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).

Custom Parameters
  • --outseq = alldata_annotation_rrna.fa
Method: ARAGORN

a program to detect tRNA genes and tmRNA genes in nucleotide sequences

Custom Parameters
  • -m
  • -t
  • -l
  • -w
  • -seq
Method: CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies.

Custom Parameters
  • database = /mnt/store3/clustcrilab/reference/CAT/CAT_prepare_20210107/2021-01-07_CAT_database
  • taxonomy = /mnt/store3/clustcrilab/reference/CAT/CAT_prepare_20210107/2021-01-07_taxonomy

Table 1. Annotation details Download table data

Feature Counts
CDS 89185
rRNA 88
tRNA 884
tmRNA 14
tmRNA* 1

Details

Method: MetaBAT2

A robust statistical framework for reconstructing genomes from metagenomic data

Custom Parameters
  • --saveCls
  • -l
Method: CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies.

Custom Parameters
  • database = /mnt/store3/clustcrilab/reference/CAT/CAT_prepare_20210107/2021-01-07_CAT_database
  • taxonomy = /mnt/store3/clustcrilab/reference/CAT/CAT_prepare_20210107/2021-01-07_taxonomy

Citations