What it does

This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads.

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Input

This expects the output format of the "Make families" tool.

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Output

The output is a tabular file where each line corresponds to a (single) read.

The columns are:

1: barcode (both tags)
2: tag order in barcode ("ab" or "ba")
3: read mate ("1" or "2")
4: read name
5: read sequence, aligned ("-" for gaps)
6: read quality scores, aligned (" " for gaps)

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Alignments

The alignments are done using MAFFT, specifically the command

$ mafft --nuc --quiet family.fa > family.aligned.fa