ArticleNature methods2016
Comparison of high-throughput sequencing data compression tools.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 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
- Dear-OMG: An Omics-General Compression Method for Genomics, Proteomics and Metabolomics Data.Interdisciplinary sciences, computational life sciences · 2026Article
- zDUR: reference-free FASTQ compressor with high compression ratio and speed.BMC bioinformatics · 2026Article
- A benchmark study of compression software for human short-read sequence data.Scientific reports · 2025Article
- MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation.Bioinformatics (Oxford, England) · 2024Article
- Genie: the first open-source ISO/IEC encoder for genomic data.Communications biology · 2024Article
- PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering.BMC bioinformatics · 2023Article
- A novel approach to T-cell receptor beta chain (TCRB) repertoire encoding using lossless string compression.Bioinformatics (Oxford, England) · 2023Article
- Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.Patterns (New York, N.Y.) · 2022Review
- SPRISS: approximating frequent k-mers by sampling reads, and applications.Bioinformatics (Oxford, England) · 2022Article
- Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression.PLoS computational biology · 2021Article
- Disk compression of k-mer sets.Algorithms for molecular biology : AMB · 2021Article
- Representation ofJournal of computational biology : a journal of computational molecular cell biology · 2021Article
- Transcriptome Landscape of Intracellular Brucella ovis Surviving in RAW264.7 Macrophage Immune System.Inflammation · 2020Article
- IonCRAM: a reference-based compression tool for ion torrent sequence files.BMC bioinformatics · 2020Article
- Performance evaluation of lossy quality compression algorithms for RNA-seq data.BMC bioinformatics · 2020Article
- Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences.GigaScience · 2020Article
- LCQS: an efficient lossless compression tool of quality scores with random access functionality.BMC bioinformatics · 2020Article
- SPRING: a next-generation compressor for FASTQ data.Bioinformatics (Oxford, England) · 2019Article
- MassComp, a lossless compressor for mass spectrometry data.BMC bioinformatics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing (HTS) data are commonly stored as raw sequencing reads in FASTQ format or as reads mapped to a reference, in SAM format, both with large memory footprints. Worldwide growth of HTS data has prompted the development of compression methods that aim to significantly reduce HTS data size. Here we report on a benchmarking study of available compression methods on a comprehensive set of HTS data using an automated framework.
Indexed as
Identifiers
27776113What OpenQuestion holds
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.