PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index.

ABSTRACT:

Motivation

Sequence alignment is one of the first steps in many modern genomic analyses, such as variant detection, transcript abundance estimation and metagenomic profiling. Unfortunately, it is often a computationally expensive procedure. As the quantity of data and wealth of different assays and applications continue to grow, the need for accurate and fast alignment tools that scale to large collections of reference sequences persists.

Results

In this article, we introduce PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast STAR aligner, PuffAligner requires considerably less m

SUBMITTER: Almodaresi F 

PROVIDER: S-EPMC9502150 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature