sequence length distribution

Question

[evashan96]

how to check sequence length distribution of trimmed reads? (fasta). is there any tool to calculate it?

[lieven.sterck]

What have you tried so far?

why not run FastQC (again) on your cleaned reads? that report includes a length distribution plot.

EDIT. Oh, ok, you're asking it for fasta format as input, then FastQC might not be the answer, unless you still have the fastq files as well then use those as input

Answer 1

[jean.elbers]

BBMap/BBTools has a readlength.sh tool that you can you to make a readlength histogram of the reads after trimming.

Answer 2

[gb]

A bit of an old tool but you can also use PRINSEQ. They also have a webversion, but never used it.

website: http://prinseq.sourceforge.net/

Answer 3

[vivek.mathema]

Try OSTRFPD: Multifunctional tool for genome-wide short tandem repeat analysis for DNA, transcripts and amino acid sequences with integrated primer designer link: https://github.com/vivekmathema/OSTRFPD

Answer 4

[michael.ante]

Lawrence et al published FAST: FAST Analysis of Sequences Toolbox (paper | github).

There you have a tool called faslen, which annotates the fasta header with its length. To only get the length, you can run:

faslen my_test.fasta | grep \>

Cheers,

Michael