Fast lightweight accurate xenograft sorting.

ABSTRACT:

Motivation

With an increasing number of patient-derived xenograft (PDX) models being created and subsequently sequenced to study tumor heterogeneity and to guide therapy decisions, there is a similarly increasing need for methods to separate reads originating from the graft (human) tumor and reads originating from the host species' (mouse) surrounding tissue. Two kinds of methods are in use: On the one hand, alignment-based tools require that reads are mapped and aligned (by an external mapper/aligner) to the host and graft genomes separately first; the tool itself then processes the resulting alignments and quality metrics (typically BAM files) to assign each read or read pair. On the other hand, alignment-free tools work directly on the raw read data (typically FASTQ files). Rece

SUBMITTER: Zentgraf J 

PROVIDER: S-EPMC8017614 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature