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Engineering the Compression of Sequencing Reads

Kowalski, T.; Grabowski, S. P.

2020-05-02 bioinformatics
10.1101/2020.05.01.071720 bioRxiv
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MotivationFASTQ remains among the widely used formats for high-throughput sequencing data. Despite advances in specialized FASTQ compressors, they are still imperfect in terms of practical performance tradeoffs. ResultsWe present a multi-threaded version of 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. The current version, v1.2, practically preserves the compression ratio and decompression speed of the previous one, reducing the compression time by a factor of about 4-5 on a 6-core/12-thread machine. AvailabilityPgRC 1.2 can be downloaded from https://github.com/kowallus/PgRC. Contactsgrabow@kis.p.lodz.pl

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.