Cargando…

genozip: a fast and efficient compression tool for VCF files

MOTIVATION: genozip is a new lossless compression tool for Variant Call Format (VCF) files. By applying field-specific algorithms and fully utilizing the available computational hardware, genozip achieves the highest compression ratios amongst existing lossless compression tools known to the authors...

Descripción completa

Detalles Bibliográficos
Autores principales:	Lan, Divon, Tobler, Raymond, Souilmi, Yassine, Llamas, Bastien
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2020
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7332572/ https://www.ncbi.nlm.nih.gov/pubmed/32407471 http://dx.doi.org/10.1093/bioinformatics/btaa290

Ejemplares similares

Genozip: a universal extensible genomic data compressor
por: Lan, Divon, et al.
Publicado: (2021)

Insane in the vembrane: filtering and transforming VCF/BCF files
por: Hartmann, Till, et al.
Publicado: (2022)

Cutevariant: a standalone GUI-based desktop application to explore genetic variations from an annotated VCF file
por: Schutz, Sacha, et al.
Publicado: (2021)

Sparse Project VCF: efficient encoding of population genotype matrices
por: Lin, Michael F, et al.
Publicado: (2020)

VCF-kit: assorted utilities for the variant call format
por: Cook, Daniel E, et al.
Publicado: (2017)

BUSZ: compressed BUS files
por: Einarsson, Pétur Helgi, et al.
Publicado: (2023)

vcf2gwas: Python API for comprehensive GWAS analysis using GEMMA
por: Vogt, Frank, et al.
Publicado: (2021)

VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects
por: Ossio, Raul, et al.
Publicado: (2019)

Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment
por: Oliva, Adrien, et al.
Publicado: (2021)

VIVA (VIsualization of VAriants): A VCF File Visualization Tool
por: Tollefson, G. A., et al.
Publicado: (2019)

bwtool: a tool for bigWig files
por: Pohl, Andy, et al.
Publicado: (2014)

VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files
por: Hart, Steven N., et al.
Publicado: (2016)

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files
por: Sun, Xiaobo, et al.
Publicado: (2018)

fqtools: an efficient software suite for modern FASTQ file manipulation
por: Droop, Alastair P.
Publicado: (2016)

BrowseVCF: a web-based application and workflow to quickly prioritize disease-causative variants in VCF files
por: Salatino, Silvia, et al.
Publicado: (2017)

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters
por: Chu, Justin, et al.
Publicado: (2014)

Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files
por: Ebbert, Mark TW, et al.
Publicado: (2014)

vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
por: Dolin, Robert H., et al.
Publicado: (2021)

HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies
por: Wang, Xiaotao, et al.
Publicado: (2023)

re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files
por: Karabayev, Daniyar, et al.
Publicado: (2021)

LDmat: efficiently queryable compression of linkage disequilibrium matrices
por: Weiner, Rockwell J, et al.
Publicado: (2023)

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
por: Zhao, Yongan, et al.
Publicado: (2012)

Pygenomics: manipulating genomic intervals and data files in Python
por: Tamazian, Gaik, et al.
Publicado: (2023)

MFCompress: a compression tool for FASTA and multi-FASTA data
por: Pinho, Armando J., et al.
Publicado: (2014)

COSMOS: Python library for massively parallel workflows
por: Gafni, Erik, et al.
Publicado: (2014)

VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity
por: Putnam, Daniel K., et al.
Publicado: (2019)

FUSTA: leveraging FUSE for manipulation of multiFASTA files at scale
por: Delehelle, Franklin, et al.
Publicado: (2022)

orfipy: a fast and flexible tool for extracting ORFs
por: Singh, Urminder, et al.
Publicado: (2021)

Pharokka: a fast scalable bacteriophage annotation tool
por: Bouras, George, et al.
Publicado: (2022)

The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets
por: Laperle, Jonathan, et al.
Publicado: (2019)

ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data
por: Moshiri, Niema
Publicado: (2023)

A fast and memory-efficient implementation of the transfer bootstrap
por: Lutteropp, Sarah, et al.
Publicado: (2020)

GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations
por: Rademaker, Daniel T, et al.
Publicado: (2023)

MAGScoT: a fast, lightweight and accurate bin-refinement tool
por: Rühlemann, Malte Christoph, et al.
Publicado: (2022)

METAL: fast and efficient meta-analysis of genomewide association scans
por: Willer, Cristen J., et al.
Publicado: (2010)

fastGapFill: efficient gap filling in metabolic networks
por: Thiele, Ines, et al.
Publicado: (2014)

ecmtool: fast and memory-efficient enumeration of elementary conversion modes
por: Buchner, Bianca, et al.
Publicado: (2023)

MathIOmica‐MSViewer: a dynamic viewer for mass spectrometry files for Mathematica
por: Roushangar, R., et al.
Publicado: (2017)

EpiCompare: R package for the comparison and quality control of epigenomic peak files
por: Choi, Sera, et al.
Publicado: (2023)

Enabling a fast annotation process with the Table2Annotation tool
por: Larmande, Pierre, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_3ggl1c8rirg0j3ikf15tt34na0