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andersen-lab / ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
https://andersen-lab.github.io/ivar/html/
GNU General Public License v3.0
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Generate separate consensus sequence for each reference found in mpileup #62

Open gkarthik opened 4 years ago

gkarthik commented 4 years ago

Currently, ivar consensus generates a concatenated consensus if multiple references are present.

iVar should generate separate consensus sequences for each reference. This is especially useful for segmented viruses.

alephreish commented 2 years ago

Are there any updates? This behavior is somewhat unexpected as the output sequence currently contains a tail-to-head concatenation of the individual consensus sequence. The only workaround is to split the input fasta into individual sequences or to split the pileup file.