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The Top 23 Genome Analysis Open Source Projects

Open source projects categorized as Genome Analysis
Categories > Genome Analysis
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104most recent commit 3 months agopypi hgvs} Downloads
Rasusa ⭐ 156
Randomly subsample sequencing reads to a specified coverage
total releases 11most recent commit 4 months ago
Winnowmap ⭐ 131
Long read / genome alignment software
most recent commit 2 years ago
Intervene ⭐ 111
Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
total releases 30most recent commit 6 months ago
Earlgrey ⭐ 90
Earl Grey: A fully automated TE curation and annotation pipeline
most recent commit 3 months ago
Mccortex ⭐ 86
De novo genome assembly and multisample variant calling
most recent commit 5 years ago
Bacannot ⭐ 85
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
most recent commit 5 months ago
Dnabert_2 ⭐ 72
The official implementation of DNABERT-2.
most recent commit 6 months ago
Helen ⭐ 52
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
total releases 19most recent commit 3 years ago
Teamteri ⭐ 50
Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure
most recent commit 8 months ago
Gala ⭐ 45
Long-reads Gap-free Chromosome-scale Assembler
most recent commit 2 years ago
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Cogclassifier ⭐ 27
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
dependent packages 1total releases 7most recent commit 6 months agopypi cogclassifier} Downloads
Blend ⭐ 26
BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)
most recent commit a year ago
Maxatac ⭐ 24
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
total releases 8most recent commit 5 months ago
Rawhash ⭐ 23
RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39
most recent commit 5 months ago
Score Assemblies ⭐ 20
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
most recent commit 3 months ago
Mspc ⭐ 18
Using combined evidence from replicates to evaluate ChIP-seq peaks
total releases 14most recent commit 3 months ago
Codex ⭐ 17
A minimal genetic data explorer that processes all genetic information locally.
most recent commit 6 months ago
Bioutils ⭐ 16
provides common tools and lookup tables used primarily by the hgvs and uta packages
dependent packages 8total releases 62most recent commit 3 months agopypi bioutils} Downloads
Ampliconreconstructorom ⭐ 14
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
most recent commit 5 months ago
Ppspcp ⭐ 13
A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline
most recent commit 3 years ago
Nanorepeat ⭐ 13
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
total releases 7most recent commit 6 months ago
The 4 Most Depended On Genome Analysis Open Source Projects
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104latest release November 21, 2022most recent commit 3 months agopypi hgvs} Downloads
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Bioutils ⭐ 16
provides common tools and lookup tables used primarily by the hgvs and uta packages
dependent packages 8total releases 62latest release July 10, 2023most recent commit 3 months agopypi bioutils} Downloads
Cogclassifier ⭐ 27
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
dependent packages 1total releases 7latest release September 07, 2022most recent commit 6 months agopypi cogclassifier} Downloads
The 10 Latest Releases In Genome Analysis Open Source Projects
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Codonu ⭐ 13
A python project for analysis of codon usage for gene or genome analysis
total releases 8latest release October 01, 2023most recent commit 6 months ago
Bioutils ⭐ 16
provides common tools and lookup tables used primarily by the hgvs and uta packages
dependent packages 8total releases 62latest release July 10, 2023most recent commit 3 months agopypi bioutils} Downloads
Rasusa ⭐ 156
Randomly subsample sequencing reads to a specified coverage
total releases 11latest release April 06, 2023most recent commit 4 months ago
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104latest release November 21, 2022most recent commit 3 months agopypi hgvs} Downloads
Cogclassifier ⭐ 27
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
dependent packages 1total releases 7latest release September 07, 2022most recent commit 6 months agopypi cogclassifier} Downloads
Maxatac ⭐ 24
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
total releases 8latest release May 05, 2022most recent commit 5 months ago
Mspc ⭐ 18
Using combined evidence from replicates to evaluate ChIP-seq peaks
total releases 14latest release March 19, 2021most recent commit 3 months ago
Intervene ⭐ 111
Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
total releases 30latest release November 12, 2020most recent commit 6 months ago
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