dePoP is a pipeline designed for analysis of NGS-sequences of pooled samples. It identifies the carriers of rare Nucleotide Variants (NV) using sequence reads of overlapping pools, a process we called de-pooling. dePoP automatizes de-multiplexing, trimming, mapping, snp-calling of raw NGS-reads and performs de-pooling using s-dePooler - a novel java application.
dePoP is adapted for work in Linux OS.
The pipeline is Perl-based (Perl v.5) and requires no installation, but the following tools must be present in the $PATH variable:
- Bowtie2 ver 2.2 or newer
- Cutadapt ver 1.8 or newer
- samtools and bcftools ver 1.3 or newer.
The following tools are included in repository and alternatively can be installed separately and included in pipeline by defined options:
- Genome Analysis Toolkit (GATK) .
- s-dePooler
These two tools require Java8 to be installed in the system.