Open nhhaidee opened 2 years ago
I think the consensus sequences from IRMA and read mapping/variant calling should be compared using global alignment. I think Edlib would be suitable for this task. It's fairly easy to use in a Python script (see https://github.com/CFIA-NCFAD/nf-ionampliseq/blob/76f9ea377156f508fc92b218f7663099e7ae5872/bin/edlib_align.py#L18). It'd be useful to report the differences if there are any.
We should have the number of differences between the IRMA and read mapping/variant calling consensus sequences and their closest ref seqs from BLAST and variant calling, respectively.
_Originally posted by @peterk87 in https://github.com/peterk87/nf-iav-illumina/pull/8#discussion_r850535916_
I think the consensus sequences from IRMA and read mapping/variant calling should be compared using global alignment. I think Edlib would be suitable for this task. It's fairly easy to use in a Python script (see https://github.com/CFIA-NCFAD/nf-ionampliseq/blob/76f9ea377156f508fc92b218f7663099e7ae5872/bin/edlib_align.py#L18). It'd be useful to report the differences if there are any.
We should have the number of differences between the IRMA and read mapping/variant calling consensus sequences and their closest ref seqs from BLAST and variant calling, respectively.
_Originally posted by @peterk87 in https://github.com/peterk87/nf-iav-illumina/pull/8#discussion_r850535916_