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28 search results found

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Python library to facilitate genome assembly, annotation, and comparative genomics

Bioconvert ⭐ 344

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

A Python frontend to (Open Biomedical) Ontologies.

Gfatools ⭐ 181

Tools for manipulating sequence graphs in the GFA and rGFA formats

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.

Fqtools ⭐ 105

An efficient FASTQ manipulation suite

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Gff3toolkit ⭐ 68

Python programs for processing GFF3 files

Hadoop Bam ⭐ 66

Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework

Coolpuppy ⭐ 66

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

Software for predicting library complexity and genome coverage in high-throughput sequencing.

The specification of the MMTF format for biological structures

Awesome Bioinformatics Formats ⭐ 36

Curated list of bioinformatics formats and publications

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).

Bac Genomics Scripts ⭐ 28

Collection of scripts for bacterial genomics

Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics

Biotoolbox ⭐ 27

Tools for querying and analysis of genomic data

Biofmtspecimens ⭐ 26

A collection of bioinformatics file format specimens to test against

RDML data import for R

Rnftools ⭐ 13

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

Nosql Biosets ⭐ 12

index and query scripts for free reference bioinformatics datasets

Fastaio.jl ⭐ 11

Utilities to read/write FASTA format files in Julia

Readdatastores.jl ⭐ 10

Datastores for reads, not your papa's FASTQ files.

Newicktools ⭐ 9

Misc tools for newick format

Toolkit for analysis of ".hyb" format nucleotide sequence data from chimeric RNA experiments.

Read Cleaning Format Conversion ⭐ 5

Short scripts to convert or modify Bioinformatics files

bioinformatic utility libraries in python

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