amplimap 0.2.5

amplicon/smMIP mapping and analysis pipeline

amplimap is a pipeline to process and analyse short-read sequencing data from smMIP-panels or PCR-based amplicons. It was designed to support both germline variant calling as well as quantification of variant allele frequencies using ultra-high-coverage pileups with and without UMIs.

amplimap takes fastq or bam files generated from an Illumina sequencer (tested with MiSeq, HiSeq, and NextSeq), assigns each read pair to a probe/amplicon, trims and aligns the reads and then generates a set of basic statistics. After that, two different types of analyses can be performed:

1. Germline variant calling using Platypus/GATK and annotation with Annovar, to generate an annotated table of potentially pathogenic variants.

2. Per-basepair “pileup” of reads to generate nucleotide counts of each base at each target basepair and each sample, for analysis of allele frequencies.

Built on top of Snakemake and Python 3, amplimap is entirely automated and can be run on a single machine as well as on a HPC cluster (eg. LSF, SGE).

• Github: https://github.com/koelling/amplimap/

• Documentation: https://amplimap.readthedocs.io/