Thanks GenoMax, I will try those tools.
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Statistics for bins
Hello everyone,
I’m working with several dozen metagenomic bins and need to analyze contig/scaffold length distributions within each bin. Specifically, I’d like to calculate:
Individual lengths of all scaffolds/contigs per bin,
Summary statistics (average, min, max lengths) of all scaffolds/contigs per bin,
Data in table format for plotting (e.g., histograms of Distribution of contig lengths in bins).
I’ve tried:
statswrapper.sh (BBMap): Provides metrics like scaf_max/ctg_max (longest scaffold/contig), but lacks per-sequence lengths or distributions.
QUAST: Excellent for assemblies, but seems cumbersome for many bins and doesn’t output per-bin length tables easily.
I would appreciate any help! Best, Alla
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GenoMax
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shevch2009 •
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shevch2009 •
1 answer
Try seqkit (specifically stats) : https://bioinf.shenwei.me/seqkit/usage/#stats
For per-sequence lengths or distributions
seqkit fx2tab --length --name --header-line foo.fasta
readlength.sh from BBMap suite can also create a read distribution histogram.
The next code didn't provides what I need
seqkit fx2tab --length --name --header-line foo.fasta
I got strange table
k127_5845587 2388
k127_1599072 5710
k127_4786624 15259
k127_2662662 8275
k127_537890 25137
k127_538940 24838
k127_4260329 30297
k127_6916585 23944
Which is no use at all for me)
And readlength.sh from BBMap workes only with raw reads and one file at a time if I am not mistaken...
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shevch2009 •
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shevch2009 •
k127_5845587 2388
k127_1599072 5710
k127_4786624 15259
That is the name of the fasta header followed by length of the sequence in the multi fasta used as input. How is that strange?
readlength.sh from BBMap workes only with raw reads and one file at a time if I am not mistaken...
Run it on all contigs via a for loop, one file at a time.
It seems I have found a solution, but without an individual lengths of all scaffolds/contigs per bin....
seqkit stats -a -T /reassembled_bins/*.fa > bin_stats.tsv
This gave me: min_len, avg_len, max_len of contigs, I can work with that :)
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