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Applications

Experiments

Open Sustainable Technology

https://github.com/althonos/pyopal

Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
bioinformatics cython-library cython-wrapper genomics needleman-wunsch python-bindings python-library sequence-alignment simd smith-waterman
Added: 11 months ago - Last Synced: 11 months ago - Created: October 04, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 64
  • Committers: 1
  • Issues: 6
  • Pull Requests: 1
  • Owner: althonos
  • Stars: 7
  • Forks: 1
  • Packages: 1
  • Downloads: 3,127
https://github.com/althonos/pyfamsa

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
bioinformatics cython-library genomics multiple-sequence-alignment python-bindings python-library sequence-alignment
Added: 11 months ago - Last Synced: 11 months ago - Created: July 28, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 83
  • Committers: 1
  • Issues: 4
  • Pull Requests: 0
  • Owner: althonos
  • Stars: 21
  • Forks: 3
  • Packages: 1
  • Downloads: 1,606
https://github.com/althonos/lightmotif

A lightweight platform-accelerated library for biological motif scanning using position weight matrices.
bioinformatics genomics pssm rust-library sequence-analysis sequence-motif simd
Added: 11 months ago - Last Synced: 11 months ago - Created: April 30, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Rust
  • Commits:
  • Committers:
  • Issues: 0
  • Pull Requests: 4
  • Owner: althonos
  • Stars: 36
  • Forks: 2
  • Packages: 6
  • Downloads: 13,920
https://github.com/vini2/phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
assembly-graphs bacteriophages bioinformatics genomics metagenomics
Added: over 1 year ago - Last Synced: 11 months ago - Created: July 21, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 545
  • Committers: 2
  • Issues: 37
  • Pull Requests: 15
  • Owner: Vini2
  • Stars: 64
  • Forks: 6
  • Packages: 1
  • Downloads: 57
https://github.com/zhengxwen/gdsfmt

R Interface to CoreArray Genomic Data Structure (GDS) Files (Development version only)
bioinformatics gds-format genomics infrastructure r
Added: over 1 year ago - Last Synced: 11 months ago - Created: June 08, 2014

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: C
  • Commits: 532
  • Committers: 7
  • Issues: 43
  • Pull Requests: 3
  • Owner: zhengxwen
  • Stars: 18
  • Forks: 4
  • Packages: 1
  • Downloads: 211,341
https://github.com/sbg/mitty

Seven Bridges Genomics aligner/caller debugging and analysis tools
bioinformatics genomics simulator
Added: over 1 year ago - Last Synced: 11 months ago - Created: August 10, 2016

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 482
  • Committers: 4
  • Issues: 13
  • Pull Requests: 3
  • Owner: sbg
  • Stars: 13
  • Forks: 2
  • Packages: 1
  • Downloads: 18
https://github.com/jlsteenwyk/orthosnap

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
bioinformatics evolution evolutionary-biology genomics orthology orthology-assignments orthology-inference phylogenetics phylogenomics python
Added: over 1 year ago - Last Synced: 11 months ago - Created: February 28, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 108
  • Committers: 2
  • Issues: 8
  • Pull Requests: 4
  • Owner: JLSteenwyk
  • Stars: 19
  • Forks: 1
  • Packages: 1
  • Downloads: 81
https://github.com/fulcrumgenomics/fgbio

Tools for working with genomic and high throughput sequencing data.
analyzing-genomic-data bioinformatics fgbio genomics molecular-indexes ngs scala umi
Added: over 1 year ago - Last Synced: 11 months ago - Created: March 03, 2016

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Scala
  • Commits: 646
  • Committers: 17
  • Issues: 112
  • Pull Requests: 73
https://github.com/ygidtu/trackplot

trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.
bioinformatics genomics python
Added: over 1 year ago - Last Synced: 11 months ago - Created: April 27, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 261
  • Committers: 3
  • Issues: 8
  • Pull Requests: 88
  • Owner: ygidtu
  • Stars: 64
  • Forks: 8
  • Packages: 1
  • Downloads: 159
https://github.com/google/nucleus

Python and C++ code for reading and writing genomics data.
bioinformatics dna genomics tensorflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: March 26, 2018

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: C++
  • Commits: 445
  • Committers: 11
  • Issues: 43
  • Pull Requests: 3
  • Owner: google
  • Stars: 777
  • Forks: 125
  • Packages: 1
  • Downloads: 238
https://github.com/dereneaton/ipyrad

Interactive assembly and analysis of RAD-seq data sets
assembly genomics phylogeny rad-seq
Added: over 1 year ago - Last Synced: 11 months ago - Created: October 07, 2015

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Jupyter Notebook
  • Commits: 3925
  • Committers: 28
  • Issues: 149
  • Pull Requests: 7
  • Owner: dereneaton
  • Stars: 70
  • Forks: 39
  • Packages: 2
https://github.com/core-bioinformatics/clustassess

Tools for assessing clustering robustness
bioinformatics clustering genomics machine-learning parameter-optimization robustness single-cell unsupervised-learning
Added: over 1 year ago - Last Synced: 11 months ago - Created: March 26, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 177
  • Committers: 4
  • Issues: 5
  • Pull Requests: 0
https://github.com/nf-core/bactmap

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
bacteria bacterial bacterial-genome-analysis genomics mapping nextflow nf-core phylogeny pipeline tree workflow
Added: over 1 year ago - Last Synced: 11 months ago - Created: June 09, 2019

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Nextflow
  • Commits: 225
  • Committers: 8
  • Issues: 25
  • Pull Requests: 42
  • Owner: nf-core
  • Stars: 48
  • Forks: 27
  • Packages: 0
https://github.com/genomicmedlab/cool-seq-tool


bioinformatics genomics
Added: over 1 year ago - Last Synced: 11 months ago - Created: September 28, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 262
  • Committers: 5
  • Issues: 123
  • Pull Requests: 113
  • Owner: GenomicMedLab
  • Stars: 4
  • Forks: 0
  • Packages: 1
  • Downloads: 2,116
https://github.com/stephenturner/kgp

1000 Genomes Project Metadata R Package
1000genomes bioinformatics genetics genomics metadata population-genetics sequencing
Added: over 1 year ago - Last Synced: 11 months ago - Created: September 09, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 30
  • Committers: 1
  • Issues: 7
  • Pull Requests: 2
  • Owner: stephenturner
  • Stars: 18
  • Forks: 3
  • Packages: 1
  • Downloads: 184
https://github.com/Gabaldonlab/redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
assembled-contigs assembly bioinformatics closing contigs docker-image fasta gap genome-assembly genomics heterozygous mate-pairs paired-end pipeline polymorphic python scaffolding
Added: over 1 year ago - Last Synced: 11 months ago - Created: April 07, 2015

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: C++
  • Commits: 560
  • Committers: 12
  • Issues: 102
  • Pull Requests: 6
https://github.com/hclimente/martini

🍸R version of SConES, a systems-biology approach to GWAS.
bioinformatics genomics gwas network-analysis r-package snps systems-biology
Added: over 1 year ago - Last Synced: 11 months ago - Created: April 06, 2017

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 469
  • Committers: 9
  • Issues: 5
  • Pull Requests: 5
  • Owner: hclimente
  • Stars: 4
  • Forks: 2
  • Packages: 1
  • Downloads: 8,048
https://github.com/jlsteenwyk/phykit

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
bioinformatics evolution evolutionary-biology genomics multiple-sequence-alignments phylogenetics phylogenomics python
Added: over 1 year ago - Last Synced: 11 months ago - Created: May 12, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 343
  • Committers: 8
  • Issues: 4
  • Pull Requests: 19
  • Owner: JLSteenwyk
  • Stars: 53
  • Forks: 7
  • Packages: 1
  • Downloads: 377
https://github.com/chrovis/cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure
2bit bam bcf bed bigwig bioinformatics clojure fasta fastq genomics gff sam vcf wig
Added: over 1 year ago - Last Synced: 11 months ago - Created: January 08, 2014

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Clojure
  • Commits: 1270
  • Committers: 17
  • Issues: 17
  • Pull Requests: 125
  • Owner: chrovis
  • Stars: 88
  • Forks: 12
  • Packages: 1
  • Downloads: 17,635
https://github.com/mbhall88/tbpore

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
bioinformatics drug-resistance-prediction genomics mycobacterium-tuberculosis nanopore variant-calling
Added: over 1 year ago - Last Synced: 11 months ago - Created: November 25, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 261
  • Committers: 4
  • Issues: 42
  • Pull Requests: 13
  • Owner: mbhall88
  • Stars: 11
  • Forks: 2
  • Packages: 1
  • Downloads: 75
https://github.com/becavin-lab/bacnet

BACNET is a Java based platform to develop website for multi-omics analysis
bacnet bioinformatics data-visualization genomics listeria multi-omics proteomics transcriptomics website
Added: over 1 year ago - Last Synced: 11 months ago - Created: April 02, 2019

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Java
  • Commits: 179
  • Committers: 11
  • Issues: 39
  • Pull Requests: 27
https://github.com/jlsteenwyk/biokit

a versatile toolkit for processing and analyzing diverse types of sequence data
bioinformatics comparative-genomics evolution evolutionary-biology evolutionary-genomics genomics python
Added: over 1 year ago - Last Synced: 11 months ago - Created: August 04, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 157
  • Committers: 2
  • Issues: 1
  • Pull Requests: 4
  • Owner: JLSteenwyk
  • Stars: 20
  • Forks: 9
  • Packages: 1
  • Downloads: 183
https://github.com/jlsteenwyk/clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
bioinformatics evolution evolutionary-biology genomics phylogenetics phylogenomics python systematics
Added: over 1 year ago - Last Synced: 11 months ago - Created: April 11, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 266
  • Committers: 8
  • Issues: 17
  • Pull Requests: 35
  • Owner: JLSteenwyk
  • Stars: 54
  • Forks: 4
  • Packages: 1
  • Downloads: 480
https://github.com/hku-bal/clairs-to

ClairS-TO - a deep-learning method for tumor-only somatic variant calling
bioinformatics deep-learning genomics illumina long-read-sequencing long-reads nanopore ont pacbio snvs somatic-mutations somatic-variants tumor-only tumors variant-calling variants
Added: over 1 year ago - Last Synced: 11 months ago - Created: November 07, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 76
  • Committers: 6
  • Issues: 1
  • Pull Requests: 2
  • Owner: HKU-BAL
  • Stars: 32
  • Forks: 2
  • Packages: 0
https://github.com/fpusan/superpang

Non-redundant pangenome assemblies from multiple genomes or bins
bioinformatics genomics metagenomics pangenome
Added: over 1 year ago - Last Synced: 11 months ago - Created: June 14, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 89
  • Committers: 1
  • Issues: 11
  • Pull Requests: 1
  • Owner: fpusan
  • Stars: 13
  • Forks: 2
  • Packages: 1
  • Downloads: 25
https://github.com/WrightonLabCSU/DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
annotation bioinformatics genomics metagenome-assembled-genomes metagenomics microbiome viral-genomics viral-metagenomics
Added: over 1 year ago - Last Synced: 11 months ago - Created: February 11, 2019

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 765
  • Committers: 18
  • Issues: 165
  • Pull Requests: 12
https://github.com/brentp/cyvcf2

cython + htslib == fast VCF and BCF processing
bioinformatics cython genomics htslib vcf
Added: over 1 year ago - Last Synced: 11 months ago - Created: August 12, 2015

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Cython
  • Commits: 461
  • Committers: 42
  • Issues: 96
  • Pull Requests: 50
  • Owner: brentp
  • Stars: 357
  • Forks: 71
  • Packages: 3
  • Downloads: 86,704
https://github.com/gmod/jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
bioinformatics genomics jbrowse visualization
Added: over 1 year ago - Last Synced: 11 months ago - Created: October 05, 2018

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: TypeScript
  • Commits: 8101
  • Committers: 33
  • Issues: 829
  • Pull Requests: 889
  • Owner: GMOD
  • Stars: 192
  • Forks: 60
  • Packages: 45
  • Downloads: 34,392
https://github.com/xinglab-ai/genomap

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)
bioinfomatics-pipeline bioinformatics bioinformatics-tool biomarker-discovery biomarkers cell-annotation classification-algorithm data-classification deep-learning genomic-data-analysis genomics genomics-visualization multi-omic-integration regression-algorithms single-cell tabular-data trajectory-inference visualization
Added: over 1 year ago - Last Synced: 11 months ago - Created: January 14, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 108
  • Committers: 6
  • Issues: 1
  • Pull Requests: 45
  • Owner: xinglab-ai
  • Stars: 11
  • Forks: 2
  • Packages: 1
  • Downloads: 178