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The Top 23 Format Bioinformatics Open Source Projects

Open source projects categorized as Format Bioinformatics
Categories > Data Processing > Bioinformatics
Csvtk ⭐ 923
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
dependent packages 1total releases 83most recent commit 3 months ago
Jcvi ⭐ 650
Python library to facilitate genome assembly, annotation, and comparative genomics
dependent packages 1total releases 97most recent commit 4 months agopypi jcvi} Downloads
Bioconvert ⭐ 344
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
total releases 34most recent commit 5 months ago
Pronto ⭐ 212
A Python frontend to (Open Biomedical) Ontologies.
dependent packages 27total releases 76most recent commit 7 months agopypi pronto} Downloads
Gfatools ⭐ 181
Tools for manipulating sequence graphs in the GFA and rGFA formats
most recent commit 6 months ago
Edamontology ⭐ 110
EDAM is an ontology of bioscientific data analysis and data management. EDAM concentrates on topics, operations, types of data, and data formats related to analysis, modelling, optimisation, and data life-cycle in biosciences, and in other research and science-based applications.
most recent commit 7 months ago
Fqtools ⭐ 105
An efficient FASTQ manipulation suite
most recent commit 4 years ago
Hickit ⭐ 69
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
most recent commit 3 years ago
Gff3toolkit ⭐ 68
Python programs for processing GFF3 files
dependent packages 1total releases 12most recent commit 6 months agopypi gff3tool} Downloads
Hadoop Bam ⭐ 66
Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework
dependent packages 33total releases 17most recent commit 5 years ago
Coolpuppy ⭐ 66
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
total releases 23most recent commit 3 months ago
Preseq ⭐ 57
Software for predicting library complexity and genome coverage in high-throughput sequencing.
most recent commit 2 years ago
Mmtf ⭐ 43
The specification of the MMTF format for biological structures
most recent commit 3 months ago
Awesome Bioinformatics Formats ⭐ 36
Curated list of bioinformatics formats and publications
most recent commit 5 years ago
Kraken Biom ⭐ 33
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
total releases 1most recent commit 2 years ago
Bac Genomics Scripts ⭐ 28
Collection of scripts for bacterial genomics
most recent commit 4 years ago
Biodata ⭐ 27
Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics
dependent packages 5total releases 79most recent commit 3 months ago
Biotoolbox ⭐ 27
Tools for querying and analysis of genomic data
most recent commit 7 months ago
Biofmtspecimens ⭐ 26
A collection of bioinformatics file format specimens to test against
most recent commit 4 years ago
Rdml ⭐ 20
RDML data import for R
dependent packages 3total releases 10most recent commit 2 years ago
Rnftools ⭐ 13
RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
total releases 26most recent commit 5 years ago
Nosql Biosets ⭐ 12
index and query scripts for free reference bioinformatics datasets
most recent commit a year ago
Fastaio.jl ⭐ 11
Utilities to read/write FASTA format files in Julia
most recent commit 7 months ago
The 7 Most Depended On Format Bioinformatics Open Source Projects
Pronto ⭐ 212
A Python frontend to (Open Biomedical) Ontologies.
dependent packages 27total releases 76latest release August 17, 2023most recent commit 7 months agopypi pronto} Downloads
Biodata ⭐ 27
Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics
dependent packages 5total releases 79latest release November 20, 2023most recent commit 3 months ago
Rdml ⭐ 20
RDML data import for R
dependent packages 3total releases 10latest release June 25, 2019most recent commit 2 years ago
Gff3toolkit ⭐ 68
Python programs for processing GFF3 files
dependent packages 1total releases 12latest release December 14, 2021most recent commit 6 months agopypi gff3tool} Downloads
Jcvi ⭐ 650
Python library to facilitate genome assembly, annotation, and comparative genomics
dependent packages 1total releases 97latest release August 30, 2023most recent commit 4 months agopypi jcvi} Downloads
Csvtk ⭐ 923
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
dependent packages 1total releases 83latest release November 27, 2023most recent commit 3 months ago
The 10 Latest Releases In Format Bioinformatics Open Source Projects
Csvtk ⭐ 923
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
dependent packages 1total releases 83latest release November 27, 2023most recent commit 3 months ago
Biodata ⭐ 27
Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics
dependent packages 5total releases 79latest release November 20, 2023most recent commit 3 months ago
Jcvi ⭐ 650
Python library to facilitate genome assembly, annotation, and comparative genomics
dependent packages 1total releases 97latest release August 30, 2023most recent commit 4 months agopypi jcvi} Downloads
Pronto ⭐ 212
A Python frontend to (Open Biomedical) Ontologies.
dependent packages 27total releases 76latest release August 17, 2023most recent commit 7 months agopypi pronto} Downloads
Coolpuppy ⭐ 66
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
total releases 23latest release July 11, 2023most recent commit 3 months ago
Gff3toolkit ⭐ 68
Python programs for processing GFF3 files
dependent packages 1total releases 12latest release December 14, 2021most recent commit 6 months agopypi gff3tool} Downloads
Rdml ⭐ 20
RDML data import for R
dependent packages 3total releases 10latest release June 25, 2019most recent commit 2 years ago
Rnftools ⭐ 13
RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
total releases 26latest release October 17, 2018most recent commit 5 years ago
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