CLERIC.md

Cleric - Swap BAM alignment reference

Install

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

Input data

Cleric operates on aligned records in the BAM format, the original reference and the target reference as FASTA. BAM file have to PacBio-compliant, meaning, cigar M is forbidden. Two sequences have to be provided, either in individual files or combined in one. The header of the original reference must match the reference name in the BAM.

Scope

Current scope of Cleric is converting a given alignment to a different reference. This is done by aligning the original and target reference sequences. A transitive alignment is used to generate the new alignment.

Output

Cleric provides a BAM file with the file named as provided via the last argument.

Example

Simple example:

cleric m530526.align.bam reference.fasta new_ref.fasta cleric_output.bam

Or:

cat reference.fasta new_ref.fasta > combined.fasta
cleric m530526.align.bam combined.fasta cleric_output.bam

FAQ

Cleric does not finish.

Runtime is linear in the number of reads provided. The alignment step runs a Needleman-Wunsch; with NxM runtime. Please do not provide references with lengths of human chromosomes, but concentrate on your actual amplicon target.