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bioRxiv · 10.1101/2022.01.04.474935

ABRIDGE: An ultra-compression software for SAM alignment files

Banerjee, S.·Andorf, C.
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Abstract

Advancement in technology has enabled sequencing machines to produce vast amounts of genetic data, causing an increase in storage demands. Most genomic software utilizes read alignments for several purposes including transcriptome assembly and gene count estimation. Herein we present, ABRIDGE, a state-of-the-art compressor for SAM alignment files offering users both lossless and lossy compression options. This reference-based file compressor achieves the best compression ratio among all compression software ensuring lower space demand and faster file transmission. Central to the software is a novel algorithm that retains non-redundant information. This new approach has allowed ABRIDGE to achieve a compression 16% higher than the second-best compressor for RNA-Seq reads and over 35% for DNA-Seq reads. ABRIDGE also offers users the option to randomly access location without having to decompress the entire file. ABRIDGE is distributed under MIT license and can be obtained from GitHub (https://github.com/sagnikbanerjee15/Abridge) and docker hub. We anticipate that the user community will adopt ABRIDGE within their existing pipeline encouraging further research in this domain.

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Banerjee, S., Andorf, C.. 2022-01-05. ABRIDGE: An ultra-compression software for SAM alignment files. https://doi.org/10.1101/2022.01.04.474935

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