Biology subjects

Debudaj-Grabysz, A.

Publications and source records attributed to Debudaj-Grabysz, A..

2 recordsLinked to original sources

bioRxiv2017

MSAC: Compression of multiple sequence alignment files

MotivationBioinformatics databases grow rapidly and achieve values hardly to imagine a decade ago. Among numerous bioinformatics processes generating hundreds of GB is multiple sequence alignments of protein families. Its largest database, i.e., Pfam, consumes 40-230 GB, depending of the variant. Storage and transfer of such massive data has become a challenge.\n\nResultsWe propose a novel compression algorithm, MSAC (Multiple Sequence Alignment Compressor), designed especially for aligned data. It is based on a generalisation of the positional Burrows-Wheeler transform for non-binary alphabets. MSAC handles FASTA, as well as Stockholm files. It offers up to six times better compression ratio than other commonly used compressors, i.e., gzip. Performed experiments resulted in an analysis of the influence of a protein family size on the compression ratio.\n\nAvailabilityMSAC is available for free at https://github.com/refresh-bio/msac and http://sun.aei.polsl.pl/REFRESH/msac.\n\nContactsebastian.deorowicz@polsl.pl\n\nSupplementary materialSupplementary data are available at the publisher Web site.

bioinformatics↗

bioRxiv2017

Whisper: Read sorting allows robust mapping of sequencing data

MotivationMapping reads to a reference genome is often the first step in a sequencing data analysis pipeline. Mistakes made at this computationally challenging stage cannot be recovered easily.\n\nResultsWe present Whisper, an accurate and high-performant mapping tool, based on the idea of sorting reads and then mapping them against suffix arrays for the reference genome and its reverse complement. Employing task and data parallelism as well as storing temporary data on disk result in superior time efficiency at reasonable memory requirements. Whisper excels at large NGS read collections, in particular Illumina reads with typical WGS coverage. The experiments with real data indicate that our solution works in about 15% of the time needed by the well-known Bowtie2 and BWA-MEM tools at a comparable accuracy (validated in variant calling pipeline).\n\nAvailabilityWhisper is available for free from https://github.com/refresh-bio/Whisper or http://sun.aei.polsl.pl/REFRESH/Whisper/\n\nContactsebastian.deorowicz@polsl.pl\n\nSupplementary informationSupplementary data are available at publisher Web site.

bioinformatics↗