About: Puffaligner: An Efficient and Accurate Aligner Based on the Pufferfish Index

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Puffaligner: An Efficient and Accurate Aligner Based on the Pufferfish Index
Creator	Almodaresi, Fatemeh Patro, Rob Zakeri, Mohsen
source	BioRxiv
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 persists. Results In this paper, 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 memory to construct its index and align reads. PuffAligner strikes a desirable balance with respect to the time, space, and accuracy tradeoffs made by different alignment tools, and provides a promising foundation on which to test new alignment ideas over large collections of sequences. Availability PuffAligner is a free and open-source software. It is implemented in C++14 and can be obtained from https://github.com/COMBINE-lab/pufferfish/tree/cigar-strings
has issue date	2020-08-12(xsd:dateTime)
bibo:doi	10.1101/2020.08.11.246892
has license	biorxiv
sha1sum (hex)	93ce4e37c77e5d9a2ab62c552af4684238a0f324
schema:url	https://doi.org/10.1101/2020.08.11.246892
resource representing a document's title	Puffaligner: An Efficient and Accurate Aligner Based on the Pufferfish Index
schema:publication	bioRxiv
resource representing a document's body	covid:93ce4e37c77e5d9a2ab62c552af4684238a0f324#body_text
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