ArticleBioinformatics (Oxford, England)2015
Reference-based compression of short-read sequences using path encoding.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- OReO: optimizing read order for practical compression.Bioinformatics advances · 2025Article
- Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression.PLoS computational biology · 2021Article
- Tackling the Challenges of FASTQ Referential Compression.Bioinformatics and biology insights · 2019Article
- Integrating long-range connectivity information into de Bruijn graphs.Bioinformatics (Oxford, England) · 2018Article
- Optimal compressed representation of high throughput sequence data via light assembly.Nature communications · 2018Article
- BdBG: a bucket-based method for compressing genome sequencing data with dynamic de Bruijn graphs.PeerJ · 2018Article
- ARSDA: A New Approach for Storing, Transmitting and Analyzing Transcriptomic Data.G3 (Bethesda, Md.) · 2017Article
- Comparison of high-throughput sequencing data compression tools.Nature methods · 2016Article
- Novel bioinformatic developments for exome sequencing.Human genetics · 2016Review
- Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph.BMC bioinformatics · 2015Article
- Data-dependent bucketing improves reference-free compression of sequencing reads.Bioinformatics (Oxford, England) · 2015Article
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Authors and funding
2 authors.
Funding
Abstract
motivationStoring, transmitting and archiving data produced by next-generation sequencing is a significant computational burden. New compression techniques tailored to short-read sequence data are needed.
resultsWe present here an approach to compression that reduces the difficulty of managing large-scale sequencing data. Our novel approach sits between pure reference-based compression and reference-free compression and combines much of the benefit of reference-based approaches with the flexibility of de novo encoding. Our method, called path encoding, draws a connection between storing paths in de Bruijn graphs and context-dependent arithmetic coding. Supporting this method is a system to compactly store sets of kmers that is of independent interest. We are able to encode RNA-seq reads using 3-11% of the space of the sequence in raw FASTA files, which is on average more than 34% smaller than competing approaches. We also show that even if the reference is very poorly matched to the reads that are being encoded, good compression can still be achieved. AVAILABILITY AND IMPLEMENTATION: Source code and binaries freely available for download at http://www.cs.cmu.edu/∼ckingsf/software/pathenc/, implemented in Go and supported on Linux and Mac OS X.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.