Description

Disambiguates reads aligned to two different organisms (e.g. human and mouse) from the same source of FASTQ files. Useful in explant RNA/DNA-Seq workflows where reads from two species are present. For reads aligned to both organisms, the algorithm compares alignment quality scores to determine the most likely species of origin. Produces four BAM files (uniquely assigned to species A or B, ambiguous for species A or B) and a summary file.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

ngs-disambiguate Documentation

Disambiguation algorithm for reads aligned to two different organisms using Tophat, Hisat2, BWA or STAR alignments.

doi: 10.12688/f1000research.10082.2License: MIT
Authors