contig_info
contig_info is a command line program written in Bash for quickly estimating several standard descriptive statistics from FASTA-formatted contig files inferred by de novo genome assembly methods. Estimated statistics are:
▹ sequence number,
▹ nucleotide residue counts,
▹ AT- and GC-content,
▹ sequence lengths,
▹ auN (also called E-size, Salzberg et al. 2012) or auNG,
▹ N50 (Lander et al. 2001) and the related N75 and N90 (e.g. Reinhardt et al. 2009, Craig Venter et al. 2001),
▹ L50 and the related L75 and L90,
▹ NG50 (Earl et al. 2011) and the related NG75, NGG90, LG50, LG75, LG90.
contig_info can also compute nucleotide content statistics for each contig sequence.
Installation and execution
Give the execute permission to the file contig_info.sh by typing:
chmod +x contig_info.shand run it with the following command line model:
./contig_info.sh [options]Usage
Run contig_info without option to read the following documentation:
USAGE: contig_info.sh [options] <contig_files>
where 'options' are:
-m <int> minimum contig length; every contig sequence of length shorter
than this cutoff will be discarded (default: 1)
-g <int> expected genome size for computing auNG and {N,L}G{50,75,90}
values instead of auN and {N,L}{50,75,90} ones, respectively
-r residue content statistics for each contig sequence instead of
global statistics
-t tab-delimited output
-h prints this help and exitsExamples
The following Bash command lines enable to download the genome sequences of the 5 Mucor circinelloides strains 1006PhL, CBS 277.49, WJ11, B8987 and JCM 22480 from the NCBI genome repository:
NCBIFTP="wget -q -O- https://ftp.ncbi.nlm.nih.gov/sra/wgs_aux/"; Z=".1.fsa_nt.gz";
echo -e "1006PhL\tAOCY01\nCBS277.49\tAMYB01\nWJ11\tLGTF01\nB8987\tJNDM01\nJCM22480\tBCHG01" |
while read -r s a; do echo -n "$s ... ";$NCBIFTP${a:0:2}/${a:2:2}/$a/$a$Z|zcat>Mucor.$s.fasta;echo "[ok]";doneThe following command line runs contig_info.sh to analyze the first downloaded file Mucor.1006PhL.fasta:
./contig_info.sh Mucor.1006PhL.fastaleading to the following standard output:
File Mucor.1006PhL.fasta
Number of sequences 1459
Residue counts:
Number of A's 10320010 30.23 %
Number of C's 6747611 19.76 %
Number of G's 6731530 19.72 %
Number of T's 10335465 30.27 %
Number of N's 0 0.00 %
Total 34134616
%AT 60.52 %
%GC 39.48 %
Sequence lengths:
Minimum 410
Quartile 25% 1660
Median 6176
Quartile 75% 37608
Maximum 213712
Average 23395.89
Contiguity statistics:
auN 65329
N50 58982
N75 36291
N90 18584
L50 194
L75 376
L90 562The same results can be outputted in tab-delimited format using option -t:
./contig_info.sh -t Mucor.1006PhL.fasta#File Nseq Nres A C G T N %A %C %G %T %N %AT %GC Min Q25 Med Q75 Max Avg auN N50 N75 N90 L50 L75 L90
Mucor.1006PhL.fasta 1459 34134616 10320010 6747611 6731530 10335465 0 30.23% 19.76% 19.72% 30.27% 0.00% 60.52% 39.48% 410 1660 6176 37608 213712 23395.89 65329 58982 36291 18584 194 376 562Of note, the five downloaded FASTA files can be analyzed with a single command line:
./contig_info.sh -t Mucor.*.fasta#File Nseq Nres A C G T N %A %C %G %T %N %AT %GC Min Q25 Med Q75 Max Avg auN N50 N75 N90 L50 L75 L90
Mucor.1006PhL.fasta 1459 34134616 10320010 6747611 6731530 10335465 0 30.23% 19.76% 19.72% 30.27% 0.00% 60.52% 39.48% 410 1660 6176 37608 213712 23395.89 65329 58982 36291 18584 194 376 562
Mucor.B8987.fasta 2210 36700617 11096810 7247117 7233795 11122895 0 30.23% 19.74% 19.71% 30.30% 0.00% 60.55% 39.45% 206 839 2482 20727 258792 16606.61 69144 58460 30025 13274 193 416 674
Mucor.CBS277.49.fasta 21 36567582 10571030 7715901 7705901 10574750 0 28.90% 21.10% 21.07% 28.91% 0.00% 57.83% 42.17% 4155 41542 934259 3187354 6050249 1741313.42 3912950 4318338 3096690 1074709 4 7 9
Mucor.JCM22480.fasta 401 36616466 10586281 6882218 6899109 10581984 1659222 28.91% 18.79% 18.84% 28.89% 4.53% 60.57% 39.43% 1038 4814 50332 135940 659822 91312.88 229712 197059 109360 63107 61 121 183
Mucor.WJ11.fasta 2519 33065171 9974064 6559358 6556539 9975210 0 30.16% 19.83% 19.82% 30.16% 0.00% 60.34% 39.66% 430 3275 7692 18010 118704 13126.30 28368 24148 12884 5672 429 898 1455The tab-delimited output format can be useful for focusing on specific fields like, e.g. the seven contiguity statistics:
./contig_info.sh -t Mucor.*.fasta | cut -f1,22-#File auN N50 N75 N90 L50 L75 L90
Mucor.1006PhL.fasta 65329 58982 36291 18584 194 376 562
Mucor.B8987.fasta 69144 58460 30025 13274 193 416 674
Mucor.CBS277.49.fasta 3912950 4318338 3096690 1074709 4 7 9
Mucor.JCM22480.fasta 229712 197059 109360 63107 61 121 183
Mucor.WJ11.fasta 28368 24148 12884 5672 429 898 1455The option -g can be used to set an expected genome size for obtaining auNG and {N,L}G{50,75,90} statistics instead of auN and {N,L}{50,75,90} ones:
./contig_info.sh -t -g 36000000 Mucor.*.fasta | cut -f1,22-#File auN N50 N75 N90 L50 L75 L90 ExpSize
Mucor.1006PhL.fasta 61944 57499 32472 7652 210 417 692 36000000
Mucor.B8987.fasta 70490 59771 30857 15730 187 399 631 36000000
Mucor.CBS277.49.fasta 3974642 4318338 3096690 1074709 4 7 9 36000000
Mucor.JCM22480.fasta 233645 197663 113006 69531 59 117 175 36000000
Mucor.WJ11.fasta 26055 21799 9865 2445 493 1092 2146 36000000Finally, the option -r enables to obtain the residue details for each sequence within each input file.
Option -r can be used together with option -t to obtain a global view of the residue composition:
./contig_info.sh -r -t Mucor.CBS277.49.fasta#File Seq Nres A C G T N %A %C %G %T %N %AT %GC Pval
Mucor.CBS277.49.fasta AMYB01000001.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_01, whole genome shotgun sequence 6050249 1750309 1276313 1271843 1751784 0 28.92% 21.09% 21.02% 28.95% 0.00% 57.89% 42.11% 0.2610
Mucor.CBS277.49.fasta AMYB01000002.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_02, whole genome shotgun sequence 5009828 1445835 1059454 1055351 1449188 0 28.85% 21.14% 21.06% 28.92% 0.00% 57.79% 42.21% 0.2910
Mucor.CBS277.49.fasta AMYB01000003.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_03, whole genome shotgun sequence 4868387 1404688 1027031 1026257 1410411 0 28.85% 21.09% 21.08% 28.97% 0.00% 57.83% 42.17% 0.1907
Mucor.CBS277.49.fasta AMYB01000004.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_04, whole genome shotgun sequence 4318338 1250156 914240 913373 1240569 0 28.94% 21.17% 21.15% 28.72% 0.00% 57.68% 42.32% 0.8201
Mucor.CBS277.49.fasta AMYB01000005.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_05, whole genome shotgun sequence 3239665 934794 681540 688359 934972 0 28.85% 21.03% 21.24% 28.86% 0.00% 57.72% 42.28% 0.1120
Mucor.CBS277.49.fasta AMYB01000006.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_06, whole genome shotgun sequence 3187354 921853 671173 669308 925020 0 28.92% 21.05% 20.99% 29.02% 0.00% 57.95% 42.05% 0.3346
Mucor.CBS277.49.fasta AMYB01000007.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_07, whole genome shotgun sequence 3096690 894782 653220 654088 894600 0 28.89% 21.09% 21.12% 28.88% 0.00% 57.79% 42.21% 0.2955
Mucor.CBS277.49.fasta AMYB01000008.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_08, whole genome shotgun sequence 2213752 637973 467830 470692 637257 0 28.81% 21.13% 21.26% 28.78% 0.00% 57.61% 42.39% 0.6272
Mucor.CBS277.49.fasta AMYB01000009.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_09, whole genome shotgun sequence 1074709 310418 227365 225234 311692 0 28.88% 21.15% 20.95% 29.00% 0.00% 57.89% 42.11% 0.8349
Mucor.CBS277.49.fasta AMYB01000010.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_10, whole genome shotgun sequence 976311 285831 206369 203542 280569 0 29.27% 21.13% 20.84% 28.73% 0.00% 58.02% 41.98% 0.0381
Mucor.CBS277.49.fasta AMYB01000011.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_11, whole genome shotgun sequence 934259 273240 195919 194769 270331 0 29.24% 20.97% 20.84% 28.93% 0.00% 58.19% 41.81% 0.1318
Mucor.CBS277.49.fasta AMYB01000012.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_12, whole genome shotgun sequence 832466 240427 175344 173907 242788 0 28.88% 21.06% 20.89% 29.16% 0.00% 58.05% 41.95% 0.7506
Mucor.CBS277.49.fasta AMYB01000013.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_13, whole genome shotgun sequence 423239 121227 88619 87831 125562 0 28.64% 20.93% 20.75% 29.66% 0.00% 58.31% 41.69% 0.0489
Mucor.CBS277.49.fasta AMYB01000014.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_14, whole genome shotgun sequence 155282 45402 31673 31509 46698 0 29.23% 20.39% 20.29% 30.07% 0.00% 59.32% 40.68% 0.0000
Mucor.CBS277.49.fasta AMYB01000015.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_15, whole genome shotgun sequence 97977 28739 20928 20035 28275 0 29.33% 21.36% 20.44% 28.85% 0.00% 58.20% 41.80% 0.2347
Mucor.CBS277.49.fasta AMYB01000016.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_16, whole genome shotgun sequence 41542 11324 9228 9406 11584 0 27.25% 22.21% 22.64% 27.88% 0.00% 55.15% 44.85% 0.0000
Mucor.CBS277.49.fasta AMYB01000017.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_17, whole genome shotgun sequence 17493 5063 3195 3919 5316 0 28.94% 18.26% 22.40% 30.38% 0.00% 59.34% 40.66% 0.0239
Mucor.CBS277.49.fasta AMYB01000018.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_18, whole genome shotgun sequence 11355 3216 2365 2256 3518 0 28.32% 20.82% 19.86% 30.98% 0.00% 59.31% 40.69% 0.5719
Mucor.CBS277.49.fasta AMYB01000019.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_19, whole genome shotgun sequence 9869 2972 2278 2160 2459 0 30.11% 23.08% 21.88% 24.91% 0.00% 55.04% 44.96% 0.0099
Mucor.CBS277.49.fasta AMYB01000020.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_21, whole genome shotgun sequence 4662 1534 815 946 1367 0 32.90% 17.48% 20.29% 29.32% 0.00% 62.23% 37.77% 0.0002
Mucor.CBS277.49.fasta AMYB01000021.1 Mucor lusitanicus CBS 277.49 MUCCIscaffold_22, whole genome shotgun sequence 4155 1247 1002 1116 790 0 30.01% 24.11% 26.85% 19.01% 0.00% 49.03% 50.97% 0.0000Note that the last column Pval assesses the GC-content adequation between each contig and the overall file content.
Briefly, (up to) 5,000 nucleotide segments (non-overlapping, of length 200 bases) are first sampled from all the contig sequences, each being used to estimate the %GC, therefore leading to (up to) 5,000 %GC values (i.e. the set GCall) representative of the GC-content variation within the whole genome assembly.
Next, for each contig, (up to) 500 nucleotide segments (non-overlapping, of length 200 bases) are sampled, leading to (up to) 500 %GC values (i.e. the set GCseq) representative of the GC-content variation within the contig.
For each contig sequence, the adequation between GCseq and GCall is assessed using a Mann-Whitney (1947) U test.
When Pval is close to 0, the GC-content of the corresponding contig is significantly different to the overall %GC.
These U test p-values can be used to identify artefactual or particular (e.g. plasmid, mitochondrion) contigs, as such sequences often induce specific nucleotide compositions.
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