Grabowski, S. | Search bioRxiv

bioRxiv2019

PgRC: Pseudogenome based Read Compressor

MotivationThe amount of sequencing data from High-Throughput Sequencing technologies grows at a pace exceeding the one predicted by Moores law. One of the basic requirements is to efficiently store and transmit such huge collections of data. Despite significant interest in designing FASTQ compressors, they are still imperfect in terms of compression ratio or decompression resources.\n\nResultsWe present Pseudogenome-based Read Compressor (PgRC), an in-memory algorithm for compressing the DNA stream, based on the idea of building an approximation of the shortest common superstring over high-quality reads. Experiments show that PgRC wins in compression ratio over its main competitors, SPRING and Minicom, by up to 18 and 21 percent on average, respectively, while being at least comparably fast in decompression.\n\nAvailabilityPgRC can be downloaded from https://github.com/kowallus/PgRC.\n\nContacttomasz.kowalski@p.lodz.pl

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↗