Tabix: fast retrieval of sequence features from generic TAB-delimited files

By Heng Li. 2011

553 citations recorded by the source corpus.

Subfields: Biomedical Engineering, Computer Networks and Communications, Molecular Biology

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Citations in the corpus

CADD: predicting the deleteriousness of variants throughout the human genome (2018, positive): “For users only interested in a small number of SNVs, the score lookup process can now be simplified and accelerated by either retrieving pre-scored SNVs via tabix (46), or through a new interface that provides scores and annotations for a single SNV, a genomic coordinate, or ranges thereof.”
Cooler: scalable storage for Hi-C data and other genomically-labeled arrays (2019, background): “There exist compression and indexing strategies for tabular text files that mitigate these challenges to some degree by enabling random access (6).”
An integrative approach to predicting the functional effects of non-coding and coding sequence variation (2015, methodology): “We obtained CADD scores by downloading files from their website and querying mutations using Tabix (Li, 2011); for GWAVA scores, we compared results from all three of the GWAVA models ( region , tss and unmatched ) and report those that yielded the highest accuracy in our tests.”
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data (2011, unknown): “VCF files are compressed and indexed with ‘bgzip’ and ‘tabix’ (Li, 2011), respectively.”
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases (2014, methodology): “A BAM file is indexed using hierarchical binning and linear index to allow very efficient retrieval so that only one disk seek (moving the disk head to the desired location) is often required for each query [25,27].”
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration (2012, methodology): “Additionally, many tab-delimited feature formats can be converted to an indexed file using Tabix [15] or ‘igvtools’.”
VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants (2014, methodology): “A VCF object can be written out as a tabix-indexed (Heng, 2010) VCF file with writeVcf.”
Improved exome prioritization of disease genes through cross-species phenotype comparison (2014, methodology): “The individual whole-exome files were extracted from the integrated call sets (Oct. 12, 2012 release at http://ftp.1000genomes.ebi.ac.uk/vol1/ ftp/phase1/analysis_results/integrated_call_sets) using tabix (Li 2011) version 0.2.6 and VCFTools (Danecek et al. 2011) version 0.1.9.”