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Results tagged with fasta
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user 12272
To be used for questions specific tothe sequence file format `.fasta`. Please minimise usage if the question is more generally about sequence formats.
2
votes
2
answers
557
views
Checking that two multiline FASTAs are identical (allowing for different order and lower/upp...
Is there a good CLI tool that can diff two multiline fasta files, ignoring order, and comparing sequences with identical names with each other pairwise. …
- 409
6
votes
How to get strain names/ids contained in a multi FASTA file using seqkit?
The nice thing about seqkit is that the answer is really simple and memorable:
seqkit seq -n sequences.fasta
This will output a text file containing one sequence name per line:
MPX/PT0001/2022
MPX/PT …
- 409
3
votes
3
answers
1k
views
How to get strain names/ids contained in a multi FASTA file using seqkit?
FASTA files can be very big and unwieldy, especially if lines are at most 80 characters, one can't speed up browsing them by using less with -S to have one sequence every two lines. …
- 409
2
votes
1
answer
47
views
Python package or CLI tool outputting mutations of sequence with respect to reference
I'm new to bioinformatics, and I'm looking for a tool that takes two FASTA files, one containing a reference, let's call it A.fasta, the other another sequence, let's call it B.fasta, and outputs just …
- 409
3
votes
4
answers
495
views
How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?
This is how I would do it using cov-spectrum: https://lapis.cov-spectrum.org/open/v1/sample/fasta?genbankAccession=MZ039713,MZ039682,OV522182
Is there something similar for NCBI/Genbank? …
- 409