Input_POGENOM pipeline¶
This pipeline generates the required input file for POGENOM. The aim of this pipeline is to increase the reproducibility of the data analysis and to simplify the use of POGENOM, especially for large datasets. POGENOM takes as input a file of the variant call format (a VCF file). This file is generated by mapping one or several metagenomic samples ((paired) read files) against a reference genome with a read-aligner and calling variants using a variant caller. These steps are automatically done by this pipeline. The pipeline can produce VCF files for multiple genomes in parallel, and will for each genome base the variant calling only on those metagenome samples that have a coverage depth and breadth above user specified values. The pipeline can also do a quick prescreening by mapping a subset of the reads from each sample, to estimate the coverage of the samples and determine which should be included. For the mapped samples, the pipeline can downsample to a target median coverage, to avoid biases due to uneven coverage.