Paired end FASTA to single BAM file
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Would Picard be acceptable? You can do it easily with FastqToSam: https://broadinstitute.github.io/picard/command-line-overview.html#FastqToSam
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Just curiously, what are reasons one would do this?
I don't know about the original poster, but BAM is actually a more efficient file format. Check this post: http://blastedbio.blogspot.com/2011/10/fastq-must-die-long-live-sambam.html