GitHub topics: pangenome
Han-Cao/collapse-bubble
Merge structural variations (SV) for pangenome VCF
Language: Python - Size: 165 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 4 - Forks: 0
dubssieg/rs-pancat-compare
Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.
Language: Rust - Size: 2.79 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 9 - Forks: 0
marschall-lab/panacus
Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
Language: Rust - Size: 4 MB - Last synced at: 5 days ago - Pushed at: 2 months ago - Stars: 103 - Forks: 8
fpusan/SuperPang
Non-redundant pangenome assemblies from multiple genomes or bins
Language: Python - Size: 3.73 MB - Last synced at: 6 days ago - Pushed at: 11 days ago - Stars: 13 - Forks: 1
phac-nml/pangwas
A pipeline for pangenome wide association studies (panGWAS).
Language: Python - Size: 49.2 MB - Last synced at: 6 days ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 0
lh3/pangene
Constructing a pangenome gene graph
Language: C - Size: 338 KB - Last synced at: 15 days ago - Pushed at: about 2 months ago - Stars: 186 - Forks: 12
neherlab/pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
Language: C - Size: 75.7 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 103 - Forks: 7
labgem/PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
Language: Python - Size: 133 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 265 - Forks: 31
maize-genetics/phg_v2
Practical Haplotype Graph (PHG) version 2
Language: Kotlin - Size: 127 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 26 - Forks: 2
SaedSilva/GeneWhale
A Utility Tool for Pan-Genome Analysis Using Docker
Language: Kotlin - Size: 3.97 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 0
nf-core/pangenome
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
Language: Nextflow - Size: 4.25 MB - Last synced at: 14 days ago - Pushed at: 24 days ago - Stars: 88 - Forks: 19
qwx9/strangepg
strange cross-platform, performance-oriented and interactive pangenome and large graph visualization
Language: C - Size: 17.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 23 - Forks: 1
dubssieg/gfagraphs
Library to parse, edit and handle in memory GFA graphs
Language: Python - Size: 290 KB - Last synced at: 14 days ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 1
Plant-Food-Research-Open/genepal
A Nextflow pipeline for genome and pan-genome annotation
Language: Nextflow - Size: 6.88 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 11 - Forks: 7
dubssieg/pancat
Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
Language: Python - Size: 10.4 MB - Last synced at: 14 days ago - Pushed at: about 2 months ago - Stars: 32 - Forks: 1
pg-space/panspace
Embedding-based indexing for compact storage, rapid querying, and curation of bacterial pan-genomes
Language: Jupyter Notebook - Size: 22.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 0
nali321/Sequence2Branches
Sequence2Branches: Creating a species-level phylogenetic tree from paired FASTQ reads
Language: Python - Size: 81.1 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0
eead-csic-compbio/get_homologues
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
Language: Perl - Size: 79.8 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 112 - Forks: 26
sciencegenome/panbed
panbed for pangenome bed files
Language: Rust - Size: 3.91 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
SegataLab/panphlan
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
Language: Python - Size: 292 KB - Last synced at: 11 days ago - Pushed at: over 1 year ago - Stars: 45 - Forks: 6
VishnuRaghuram94/SCAPE
SCAPE - StaphyloCoccus Aureus Pangenome Exploration
Size: 30.5 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0
applicativesystem/rust-pangenome-graph-summarize
rust pangenome graph summarize
Language: Rust - Size: 3.16 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
pangenome/chromosome_communities
Recombination between heterologous human acrocentric chromosomes
Language: R - Size: 2.6 MB - Last synced at: 17 days ago - Pushed at: 11 months ago - Stars: 6 - Forks: 0
at-cg/PanAligner
Long read aligner for cyclic and acyclic pangenome graphs
Language: C - Size: 3.79 MB - Last synced at: 14 days ago - Pushed at: over 1 year ago - Stars: 36 - Forks: 4
lucianhu/Masterarbeit
Leveraging WES short reads for PAN-EXOME creation and analysis.
Language: WDL - Size: 18.6 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0
rx32940/BactPrep
Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)
Language: Python - Size: 30.9 MB - Last synced at: 7 months ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 1
SouthGreenPlatform/panache
Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.
Language: Vue - Size: 38 MB - Last synced at: 14 days ago - Pushed at: almost 2 years ago - Stars: 44 - Forks: 4
maxgmarin/panqc
A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses
Language: Python - Size: 332 KB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 16 - Forks: 0
dubssieg/pangenome-notes Fork of jackyzha0/quartz
Notes upon pangenome graphs construction
Language: TypeScript - Size: 8.64 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0
codecreatede/pangenealign.jl
julia implementation for the analysis of pangenes
Language: Julia - Size: 3.91 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
IBCHgenomic/pangenome-single-copy-gene
single copy pangenome analysis from alignments to phylogenomics
Language: Shell - Size: 2.93 KB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
longg2/LongBioinformatics
Scripts used by George S. Long
Language: Shell - Size: 368 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0
cartoonist/forgers
VCF manipulation based on FORGe ranking
Language: Rust - Size: 38.1 KB - Last synced at: 17 days ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
dcmonti/rs_graph_hash
Alignment (free) sequence to graph
Language: Rust - Size: 136 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
cjalth/pangenome_pipeline
Language: Nextflow - Size: 26.2 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0
lucaparmigiani/Pangenome-Openness
Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-mers. PCJ Math & Comp Biol. (2024).
Language: R - Size: 115 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0
dubssieg/sharepg
Analysis of shared parts of a pangenome
Language: Python - Size: 22.5 KB - Last synced at: 8 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 0
salvadorlab/mbovpan
Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.
Language: Nextflow - Size: 389 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0
kevsilva/StrainFLAIR
Strain-level abundances estimation in metagenomic samples using variation graphs
Language: Python - Size: 75.2 MB - Last synced at: 24 days ago - Pushed at: over 2 years ago - Stars: 25 - Forks: 5
bigbio/pgt-pangenome
Protegenomics analysis based on Pangenome references
Language: Jupyter Notebook - Size: 595 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
gongyh/nf-core-scp
Single Cell guided Pangenome analysis pipeline using SPAdes, CheckM, GTDB-Tk, Prokka, Roary and extensive quality control.
Language: Nextflow - Size: 2.13 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
iferres/pagoo
A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
Language: R - Size: 38.7 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 22 - Forks: 4
heringerp/oxiqle Fork of oxigraph/oxigraph
SPARQL endpoint to represent pangenomic data
Language: HTML - Size: 5.61 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1
moorembioinfo/FlexCore
Extract flexible bacterial core genome alignments and compute SNP distances. Additionally, perform rarefaction-sampling analysis of alignments
Language: Python - Size: 49.8 KB - Last synced at: 6 days ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
sablokgaurav/pacbio_hifiasm_polished
a streamline for the pacbiohifiasm and polishing and also making the contiguity maps both instance based and a snakemake code.
Size: 1.95 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
JoshuaDanielRubin/SAFARI_data
Sensitive Alignments from a RYmer Index
Language: Python - Size: 1.24 GB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
pangenome/odgi-paper
ODGI: understanding pangenome graphs (https://doi.org/10.1093/bioinformatics/btac308)
Language: TeX - Size: 10 MB - Last synced at: 17 days ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0
gaojunxuan/chrom_mini_graph
Space-efficient minimizer-based pangenome reference graph and haplotype mapping tool
Language: Rust - Size: 32.5 MB - Last synced at: 14 days ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 0
444thLiao/pangenome_workflow
luigi based workflow for analysising WGS samples collecting from different source. It will auto clustering, annotating gene or species, and finally perform pangenome analysis(roary).
Language: Python - Size: 1.24 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 0
ouzounis/figshare
datasets shared on figshare
Size: 530 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
chmccarthy/Pangloss
Pangenome analysis of eukaryotes.
Language: Perl - Size: 21 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 15 - Forks: 4
michkam89/PAPi
PAPi (Pangenome Analysis Pipeline)
Language: R - Size: 76.8 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0
songtaogui/pan-Zea_construct
Workflow to construct linear representation of pan genome from deep WGS data and public assemblies
Language: Shell - Size: 785 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 21 - Forks: 5
carleton-spacehogs/pangenome-selection
A repository as a Supplementary Methods of Moulana et al., 2019
Language: Python - Size: 5.04 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1
vjcitn/BiocHPRClk
A look at the pangenome consortium resources in AnVIL
Language: R - Size: 45 MB - Last synced at: 3 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
FarhanaRiaz123/Pangenome-Analysis
Pangenome-Analysis.py is written for extraction of core, accessory and unique genomes (Gene families and proteins) along with filtration of single copy orthologues, creation of binary and count matrices as well as removal of duplicates.
Language: Python - Size: 4.88 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0
AnimalGenomicsETH/bovine-graphs
Integrate multiple genome assemblies into a pangenome graph
Language: Python - Size: 23.4 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 18 - Forks: 6
songtaogui/panz-SV-pipe
Structure variants calling and genotyping scripts for pan-Zea
Language: Shell - Size: 75.2 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 0
songtaogui/pan-Zea_utilities
the miscellaneous analysis scripts used in the research of pan-Zea genome and genetics
Language: Shell - Size: 102 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0
SioStef/panplots
A small R script for generating pangenome accumulation curves
Language: R - Size: 4.88 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 2
D4GEN-Genopole/I-E-Pan
Développement des outils informatiques pour l'analyse de données - Projet porté par Guillame GAUTREAU - INRAE
Language: HTML - Size: 153 MB - Last synced at: 6 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0
iferres/simurg
Simulate pangenomes according to the IMG + Neutral models
Language: R - Size: 382 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 4 - Forks: 1
UPOBioinfo/crispromeskape
Scripts to analyze the data for the paper "An outstanding bacterial membranome requires CRISPR-Cas systems to avoid the intervention of phages" and derive the figures or subfigures shown in the manuscript.
Language: Python - Size: 85.6 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1
brettwhitty/bw-msu-tools
Archive of personal scripts repository from my various projects in the Buell Lab at MSU (Jan. 2008 - Apr. 2011)
Language: Perl - Size: 3.76 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
jsa-aerial/panclus
Pangenome clustering using entropy, relative entropy, cumulative RE, hybrid distributions, et.al
Language: Clojure - Size: 59.6 KB - Last synced at: 2 months ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 1
kloetzl/pangenomesim
♥ Simulate bacterial pangenomes.
Language: C++ - Size: 75.2 KB - Last synced at: about 2 years ago - Pushed at: about 7 years ago - Stars: 4 - Forks: 0
