SRPRISM (Single Read Paired Read Indel Substitution Minimizer): an efficient aligner for assemblies with explicit guarantees.

ABSTRACT:

Background

Alignment of sequence reads generated by next-generation sequencing is an integral part of most pipelines analyzing next-generation sequencing data. A number of tools designed to quickly align a large volume of sequences are already available. However, most existing tools lack explicit guarantees about their output. They also do not support searching genome assemblies, such as the human genome assembly GRCh38, that include primary and alternate sequences and placement information for alternate sequences to primary sequences in the assembly.

Findings

This paper describes SRPRISM (Single Read Paired Read Indel Substitution Minimizer), an alignment tool for aligning reads without splices. SRPRISM has features not available in most tools, such as (i) support for searc

SUBMITTER: Morgulis A 

PROVIDER: S-EPMC7172022 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature