Cutting fasta file into chunks?

Question

[zhousun21]

Hi everyone, I'm using some chromosome-level genome assemblies, which have very large sequences. I need to cut these into 1 kb chunks for an analysis.

I have looked at a variety of available tools but I don't see any that do this. Does anyone know of one?

Any advice will be appreciated.

[Fatima]

There might be a more straightforward method out there, but you can use split, and then fix the divided sequences (first & last sequences)

 split -b 1k myfile segment

[Joe]

Are we sure this works? split is a standard unix tool which has no understanding of base pairs. You may be confusing the split with kilobytes. split doesn't understand anything about fasta file headers etc to my knowledge.

[zhousun21]

Thank you, this works!

[Ram]

The second step sounds complicated. How woulld you clean up these "divided" sequences and still maintain a file size of 1 kb across the board?

[zhousun21]

Thank you everyone!

All useful solutions.

[Ram]

Please do not add an answer if you're not answering the principal question.

[cpad0112]

try seqkit split

Answer 1

[GenoMax]

faSplit from Jim Kent's tools. Link for linux version. chmod a+x faSplit after download.

faSplit - Split an fa file into several files.
usage:
   faSplit how input.fa count outRoot
where how is either 'about' 'byname' 'base' 'gap' 'sequence' or 'size'.  
Files split by sequence will be broken at the nearest fa record boundary. 
Files split by base will be broken at any base.  
Files broken by size will be broken every count bases.

For what you want

faSplit size input.fa 1000 outRoot

This breaks up input.fa into 1000 base chunks

[zhousun21]

This also works, thanks!

Answer 2

[shenwei356]

We use seqkit to slide on sequences with 1kb window:

seqkit sliding -s 1000 -W 1000 seqs.fa.gz -o out.fa.gz

You can also adjust step size to make interleaved chunks in some scenarios, e.g., -s 900 -W 1000 for 1kb fragments with 100bp overlap.

Usage and examples:

sliding sequences, circular genome supported

Usage:
  seqkit sliding [flags]

Flags:
  -C, --circular-genome   circular genome.
  -g, --greedy            greedy mode, i.e., exporting last subsequences even shorter than windows size
  -s, --step int          step size
  -W, --window int        window size

Answer 3

[Juke34]

Plenty of solution described here : Tutorial: FASTA file split

[Ram]

Love the comparison table!

Answer 4

[GenoMax]

Use 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.

[zhousun21]

This is perfect, thank you. I had checked bbmap but somehow this wasn't on the list of functions. But it's there anyway.

[Ram]

I don't think this would work based on file size, genomax.

[GenoMax]

Should work fine. I recall Brian using it with Rice genome.