PathSeq

We present a customizable computational tool, PathSeq2.0, to enable the discovery and identification of microbial sequences in metagenomic samples. This is a flexible, user-adaptable, pipeline that is easily assembled using a configuration file tailored towards particular sequencing experiment parameters such as type of sequencing library, sample of origin, sequencing technology, host species and library read length. PathSeq2.0 also provides auxiliary tools that facilitate the identification of viral integration sites within the host genome and quantification of microbial abundance in the sample set.