aTRAM 2.0: An Improved, Flexible Locus Assembler for NGS Data

Julie M. Allen, Raphael LaFrance, Ryan A. Folk, Kevin P. Johnson, Robert P. Guralnick

Research output: Contribution to journalReview article

Abstract

Massive strides have been made in technologies for collecting genome-scale data. However, tools for efficiently and flexibly assembling raw outputs into downstream analytical workflows are still nascent. aTRAM 1.0 was designed to assemble any locus from genome sequencing data but was neither optimized for efficiency nor able to serve as a single toolkit for all assembly needs. We have completely re-implemented aTRAM and redesigned its structure for faster read retrieval while adding a number of key features to improve flexibility and functionality. The software can now (1) assemble single-or paired-end data, (2) utilize both read directions in the database, (3) use an additional de novo assembly module, and (4) leverage new built-in pipelines to automate common workflows in phylogenomics. Owing to reimplementation of databasing strategies, we demonstrate that aTRAM 2.0 is much faster across all applications compared to the previous version.
Original languageEnglish (US)
Number of pages4
JournalEvolutionary Bioinformatics
Volume14
DOIs
StatePublished - 2018

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Workflow
Genes
Genome
loci
genome
Software
Pipelines
Databases
Technology
software
Direction compound

Keywords

  • INHS

Cite this

aTRAM 2.0: An Improved, Flexible Locus Assembler for NGS Data. / Allen, Julie M.; LaFrance, Raphael; Folk, Ryan A.; Johnson, Kevin P.; Guralnick, Robert P.

In: Evolutionary Bioinformatics, Vol. 14, 2018.

Research output: Contribution to journalReview article

Allen, Julie M. ; LaFrance, Raphael ; Folk, Ryan A. ; Johnson, Kevin P. ; Guralnick, Robert P. / aTRAM 2.0: An Improved, Flexible Locus Assembler for NGS Data. In: Evolutionary Bioinformatics. 2018 ; Vol. 14.
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