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Multimapper

License: GPL v3

This pipeline is a re-write of the multiple_mappings_to_bam.py by Simon Harris, formerly of the Bacterial Genomics team at the Wellcome Sanger Institute.

This pipeline focuses on being a quick and easy mapping software. It can run in a directory of paired lanes. So long as the pairs are identicle in prefix they can be paired.

Dependencies

  • bwa-mem2
  • python 3.7+
  • raxml-ng
  • smalt
  • samtools 1.6+
  • bowtie2

Install

To install by Dockerfile please pull the docker image from the Pathogen Informatics repository[https://hub.docker.com/u/sangerpathogens]

Otherwise clone by running the following and installing all listed dependencies.

git clone https://github.com/sanger-pathogens/multimapper.git
cd multimapper
pip3 install requirements.txt

Basic Usage

To run the pipeline in its simplest form you need a reference to map to and a folder containing paired reads.

Surface Usage Options

The pipeline has a small group of options shared across it's mappers and vcf tools. These include

--qc      if set to 'on' will produce qc readings for mapped reads
--mapper  sets the mapper from between 'smalt', 'bwa-mem2' and 'bowtie2'
--snp     either sh16 for the original conversions to bcf, or freebayes for a simpler variant calling
--k       scanning kmer length for mapping and snp calling processes
WIP: not fully functional
--pseudo  creation of pseudosequence from

Pre-set configs

The pipeline can use alternate configs, accessible using -c <my_config> on the command line. The available configs included are fast.config and a WIP full.config. Fast config removes qc and all Simon Harris processes to quickly process the data through BWA-mem2 and Freebayes. WIP Full config applies all available processing; this includes QC filtering, mapping, variant calling using Simon Harris methods and pseudosequence generation, indel trimming and phylogeny tree generation.

It can be run as shown below:

nextflow multimapper.nf -c <fast/full>.config -r <reference.fa>

Setting config guide

The nextflow.config file contained in this repo has the basic set-up showing the available tools. To build a custom run, download the nextflow.config file and edit it so suit specific pipeline requirement.

Links to external software

SMALT: documentation available near the bottom of this[https://www.sanger.ac.uk/tool/smalt-0/] page