I have aligned contigs to a reference using Bowtie2 which gives a SAM file output.
I require a mutli-fasta alignment for downstream analysis-NOT a consensus as my dataset contains unknown paralogs that I have to separate manually. I repeat i do NOT want to extract a consensus sequence, i just want a set of aligned fastas.
Is it possible to convert SAM files to an aligned multifasta, or am i going to have to do my whole alignment manually?
I require a mutli-fasta alignment for downstream analysis-NOT a consensus as my dataset contains unknown paralogs that I have to separate manually. I repeat i do NOT want to extract a consensus sequence, i just want a set of aligned fastas.
Is it possible to convert SAM files to an aligned multifasta, or am i going to have to do my whole alignment manually?
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