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  • Tool to perform alignment and consensus on specialized FASTQ dataset?

    I have sequencing data that was given molecular tags, indicating they were amplified from the same molecule and should be given a value of 1. I've been searching for a sophisticated tool or set of tools to use on a LINUX machine that are capable of aligning these groups de novo (no reference, but they are all very similar of course), then taking quality scores and maybe Kimura model parameters into account for consensus calling.

    I've tried a few methods including aligning with a dummy index with BWA followed by EMBOSS consensus calling, but these consensus reads were very insensitive and resulted in inappropriate Ns. If I convert the fastq to fasta in the beginning and just use clustalo followed by EMBOSS it gets closer, but it still is less sensitive that I'd like for consensus calling, and I'd prefer to use the quality information since I have it.

    Any suggestions are very much appreciated.

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