Galaxy |

pbmm2 (version 1.17.0+galaxy0)

Will you select a reference genome from your history or use a built-in index?:

Using reference genome:

Select genome from the list

reads:

PacBio reads in BAM or [gzipped] fasta or fastq format

Set alignment mode:

Output Options

Output Options 0

What it does

A minimap2 wrapper for PacBio data: native PacBio data in ⇨ native PacBio BAM out.

pbmm2 is Pacific Biosciences’ wrapper for minimap2’s C API. It supports native PacBio input. Output can be used directly for polishing using pbgcpp.

Input: PacBio reads in bam or [gzipped] fasta or fastq format. NOTE: to use the output of pbmm2 for pbgcpp (GenomicConsensus), you have to provide PacBio CLR reads in bam format. You can use pbmm2 to align other types of PacBio reads in [gzipped] fasta or fastq format, but you can’t use the output for pbgcpp (GenomicConsensus).

Output: A sorted PacBio BAM file, suitable for use with pbgcpp (previously known as GenomicConsensus).