I have a 10 gb .faa proteomes file that I want to run MAFFT on. But it is too big and hence I need to divide the file. How do I convert it to smaller files in windows without losing any data ? The solutions I have come across are for a UNIX/LINUX based environment
3 answers
Seqkit is the answer.
To split into 100 parts:
seqkit split myfile.faa --by-part 100
To split by number of desired sequences per file (eg 5000 per file):
seqkit split myfile.faa --by-part 5000 -by-size
The solutions I have come across are for a UNIX/LINUX based environment
Yes, use linux, if you want to perform any bioinformatics you need to use linux
You can use my Genozip tool:
genozip myfile.faa
genocat --downsample 3,1 myfile.faa.genozip <--- get part 1 out of 3
Works on Windows (as well as Linux and Mac)
See here: https://genozip.com/downsampling.html
14 methods reviewed here: https://github.com/Juke34/knowledge/blob/main/split_fasta.md
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from the statement
The solutions I have come across are for a UNIX/LINUX based environment, I am assuming that you are on windows. Even in windows (=>10), you can use GNU-linux tools using wsl2. I would suggestseqkit(windows version) from here. Please go through the manual and there are multiple ways to split a fasta using seqkit in manual.