command-line tool to split genome FASTA into equal chunks?
Say I have the file for accession LS483306.1 which is one big sequence starting with
>LS483306.1 xyz
AGCT...
and want to have one file with N sequences of size X, looking like this (example X=2000):
>LS483306.1:1-2000 xyz
AGCT...
>LS483306.1:2001-4000 xyz
GCTA...
>LS483306.1:4001-6000 xyz
CTGA...
and so on.
Is there a ready-made command-line tool for this? Which? I could write a BioPython script but I would like something faster.
1 answer
shred.sh from BBMap suite.
Usage: shred.sh in=<file> out=<file> length=<number> minlength=<number> overlap=<number>
in=<file> Input sequences.
out=<file> Destination of output shreds.
length=500 Desired length of shreds.
minlength=1 Shortest allowed shred. The last shred of each input sequence may be shorter than desired length.
overlap=0 Amount of overlap between successive reads.
reads=-1 If nonnegative, stop after this many input sequences.
equal=f Shred each sequence into subsequences of equal size of at most 'length', instead of a fixed size.
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