ArticleAlgorithms for molecular biology : AMB2013
Data compression for sequencing data.
Article in Algorithms for molecular biology : AMB, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Vertical lossless genomic data compression tools for assembled genomes: A systematic literature review.PloS one · 2020Pooled it
- FFC: a scalable FASTA compressor.Bioinformatics (Oxford, England) · 2026Article
- Efficient and robust search of microbial genomes via phylogenetic compression.Nature methods · 2025Article
- Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.Patterns (New York, N.Y.) · 2022Review
- A Hybrid Data-Differencing and Compression Algorithm for the Automotive Industry.Entropy (Basel, Switzerland) · 2022Article
- Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences.GigaScience · 2020Article
- Pattern Matching for DNA Sequencing Data Using Multiple Bloom Filters.BioMed research international · 2019Article
- Tackling the Challenges of FASTQ Referential Compression.Bioinformatics and biology insights · 2019Article
- K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.Bioinformatics (Oxford, England) · 2018Article
- Fourth Generation of Next-Generation Sequencing Technologies: Promise and Consequences.Human mutation · 2016Review
- Comparison of high-throughput sequencing data compression tools.Nature methods · 2016Article
- MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression.BMC bioinformatics · 2016Article
- Bitpacking techniques for indexing genomes: I. Hash tables.Algorithms for molecular biology : AMB · 2016Article
- Data-dependent bucketing improves reference-free compression of sequencing reads.Bioinformatics (Oxford, England) · 2015Article
- GDC 2: Compression of large collections of genomes.Scientific reports · 2015Article
- An alignment-free method to find and visualise rearrangements between pairs of DNA sequences.Scientific reports · 2015Article
- iDoComp: a compression scheme for assembled genomes.Bioinformatics (Oxford, England) · 2015Article
- MAFCO: a compression tool for MAF files.PloS one · 2015Article
- Sequence Factorization with Multiple References.PloS one · 2015Article
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
: Post-Sanger sequencing methods produce tons of data, and there is a general agreement that the challenge to store and process them must be addressed with data compression. In this review we first answer the question "why compression" in a quantitative manner. Then we also answer the questions "what" and "how", by sketching the fundamental compression ideas, describing the main sequencing data types and formats, and comparing the specialized compression algorithms and tools. Finally, we go back to the question "why compression" and give other, perhaps surprising answers, demonstrating the pervasiveness of data compression techniques in computational biology.
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Registered trials
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.