TagDust2: a generic method to extract reads from sequencing data.

ABSTRACT:

Background

Arguably the most basic step in the analysis of next generation sequencing data (NGS) involves the extraction of mappable reads from the raw reads produced by sequencing instruments. The presence of barcodes, adaptors and artifacts subject to sequencing errors makes this step non-trivial.

Results

Here I present TagDust2, a generic approach utilizing a library of hidden Markov models (HMM) to accurately extract reads from a wide array of possible read architectures. TagDust2 extracts more reads of higher quality compared to other approaches. Processing of multiplexed single, paired end and libraries containing unique molecular identifiers is fully supported. Two additional post processing steps are included to exclude known contaminants and filter out low complexit

SUBMITTER: Lassmann T 

PROVIDER: S-EPMC4384298 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature