FUSE.md

fuse - Reduce alignment into its representative sequence

Install

Install the minorseq suite using bioconda, more info here. One of the binaries is called fuse.

Input data

Fuse operates on aligned records in the BAM format. BAM files have to PacBio-compliant, meaning, cigar M is forbidden.

Scope

Current scope of Fuse is creation of a high-quality consensus sequence. Fuse includes in-frame insertions with a certain distance to each other. Major deletions are being removed.

Output

Fuse provides a FASTA file per input. Output file is provided by the second argument.

Example

Simple example:

fuse m530526.align.bam m530526.fasta

Output: m530526.fasta