DEPRECATED. This tool is no longer maintained. See MIGEC instead.
Molecular tagging approach has revolutionized the field of high depth genome re-sequencing by allowing detection of ultra-rare mutations. This pipeline aims at filling the gap in software for analysis of UMI-tagged data. MAGERI implements consensus assembly, alignment and variant calling and allows to process datasets into ready SAM and VCF files in a single command. Its main purpose is to analyze targeted region genome re-sequencing data for tumor heterogeneity and circulating tumor DNA studies, however it can be also applied to other tasks that require accurate rare variant detection.
See mageri-paper repository for examples and supplementary data.
Software binaries can be found in the releases section, the documentation is available here.
Please cite the software as Shugay et al. Plos Comp Biol 2017.