Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: pangenomics
cucapra/pollen
generating hardware accelerators for pangenomic graph queries
Language: Python - Size: 33 MB - Last synced: about 11 hours ago - Pushed: about 14 hours ago - Stars: 24 - Forks: 1
Tharos-ux/sharepg
Analysis of shared parts of a pangenome
Language: Python - Size: 20.5 KB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 0 - Forks: 0
Rowena-h/GaeumannomycesGenomics
Scripts for Hill et al. (in review) 🌾
Language: R - Size: 3.12 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 2 - Forks: 0
Tharos-ux/gfagraphs
Library to parse, edit and handle in memory GFA graphs
Language: Python - Size: 188 KB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 2 - Forks: 1
beiko-lab/arete
AMR/VF LGT focused bacterial genomics analysis workflow
Language: Python - Size: 36.7 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 19 - Forks: 4
gauravcodepro/pangenomes-metagenomes
a workflow for complete analysis of bacterial metagenomes and pagenome graphs and direct viewing in panchae. It will also analyze metagenomes from both illumina and long reads
Language: Shell - Size: 34.2 KB - Last synced: 12 days ago - Pushed: 18 days ago - Stars: 1 - Forks: 0
gauravcodepro/pangenomeMetagenomicsNormalizer
a pangenome metagenomics normalizer, given a gene ontology based presence and absence and a species file, it first summarizes the count across the species and then takes the count of the gene ontologies and present a ratio The higher the ratio the more presence of that ontology across the species.
Language: Python - Size: 140 KB - Last synced: 12 days ago - Pushed: 18 days ago - Stars: 0 - Forks: 0
GCBL-NIAB/Bos_indicus_pangenome_10X
Advancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences in Bos indicus
Size: 13.7 KB - Last synced: 19 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0
Tharos-ux/pancat
Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
Language: Python - Size: 1.74 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 28 - Forks: 1
merenlab/anvio
An analysis and visualization platform for 'omics data
Language: Python - Size: 715 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 401 - Forks: 138
AlgoLab/RecGraph
Optimal sequence-to-graph alignment with recombinations
Language: Rust - Size: 3.14 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 15 - Forks: 1
carpentries-incubator/pangenomics-python
https://czirion.github.io/pangenomics-python/
Language: Python - Size: 303 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 1
marschall-lab/panacus
Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
Language: Rust - Size: 3.31 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 57 - Forks: 4
Tharos-ux/pangenome-notes Fork of jackyzha0/quartz
Notes upon pangenome graphs construction
Language: TypeScript - Size: 8.05 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0
jorgeavilacartes/panricci
Alignment of Pangenome Graphs with Ricci Flow
Language: Jupyter Notebook - Size: 1.08 MB - Last synced: 3 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0
at-cg/minichain
Long-read aligner to pangenome graphs
Language: C - Size: 285 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 18 - Forks: 2
carpentries-incubator/topological-data-analysis
Topological data analysis for Comparative Genomics
Language: Python - Size: 10.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 1
carpentries-incubator/pangenomics
Pangenome Analysis in Prokaryotes Lesson
Language: Python - Size: 16.4 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 9 - Forks: 7
carpentries-incubator/pangenomics-workshop Fork of carpentries-lab/metagenomics-workshop
Pangenomics Workshop Overview
Language: Python - Size: 71.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 2
carpentries-incubator/shell-pangenomics Fork of carpentries-lab/metagenomics-shell
Introduction to the Command Line for Pangenomics
Language: Python - Size: 76.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 2
vinuesa/TIB-filoinfo
Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
Language: Shell - Size: 155 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 16 - Forks: 4
urbanslug/junctions
Compare pangenomes using ED-Strings
Language: C++ - Size: 3.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0
noecochetel/North_American_Vitis_Pangenome
Construct and Analyze the North American Vitis pangenome
Language: R - Size: 328 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 12 - Forks: 3
marschall-lab/GFAffix
GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
Language: Rust - Size: 5.68 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 33 - Forks: 4
algbio/GraphChainer
An accurate aligner of long reads to a variation graph, based on co-linear chaining
Language: C++ - Size: 305 KB - Last synced: 3 months ago - Pushed: about 1 year ago - Stars: 25 - Forks: 3
peng-ye/MetaPGN
A pipeline for construction and graphical visualization of annotated pangenome networks.
Language: Perl - Size: 40.4 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 13 - Forks: 5
michkam89/PAPi
PAPi (Pangenome Analysis Pipeline)
Language: R - Size: 76.8 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0
legumeinfo/gcv
Federating genomes with love (and synteny derived from functional annotations)
Language: TypeScript - Size: 13.5 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 30 - Forks: 12
lucaparmigiani/Pangenome-Openness
Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-mers. bioRxiv. (2023).
Language: R - Size: 115 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0
iFoxz17/WF_Recgraph
Optimal sequence-to-graph alignment with recombinations using wavefront algorithm.
Language: Rust - Size: 15.5 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 0
emmaewade/pangenome-workflow
A Snakemake workflow for microbial pangenomics analyses.
Language: Perl - Size: 231 KB - Last synced: 4 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 1
faylward/pangenomics
Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C-ARSC, N-ARSC, and intergenic spacer lengths are also included.
Language: Python - Size: 37.8 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 5 - Forks: 5
LilithElina/CPANG19 Fork of GTPB/CPANG19 📦
CPANG19 - Computational PANGenomics (2019)
Language: Python - Size: 43 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0
Jtrachsel/pdtools
Functions for working with NCBI's Pathogen Detection data
Language: R - Size: 6.51 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 0
darcyabjones/mumflow
A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
Language: Python - Size: 42 KB - Last synced: 29 days ago - Pushed: almost 5 years ago - Stars: 3 - Forks: 3
ccdmb/mumflow Fork of darcyabjones/mumflow
A nextflow pipeline to run the mummer pipelines (align genomes, call snps) and process outputs into sane formats.
Language: Python - Size: 43 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0
ampatzia/pasaR
Pangenomic Statistical analysis in R (pasaR)
Language: R - Size: 721 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 2 - Forks: 0
faylward/PMG
This repo contains scripts used for the identification of phylogenetic marker genes (PMGs) in assembled metagenomic data. Code is provided for benchmarking this method on sequenced genomes as well as running this analysis on metagenomic data. These scripts are in development.
Language: Python - Size: 10.1 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 1