Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: pangenome
bigbio/pgt-pangenome
Protegenomics analysis based on Pangenome references
Language: Jupyter Notebook - Size: 595 MB - Last synced: about 2 hours ago - Pushed: about 9 hours ago - Stars: 0 - Forks: 0
Tharos-ux/sharepg
Analysis of shared parts of a pangenome
Language: Python - Size: 20.5 KB - Last synced: about 3 hours ago - Pushed: 1 day ago - Stars: 0 - Forks: 0
Tharos-ux/gfagraphs
Library to parse, edit and handle in memory GFA graphs
Language: Python - Size: 188 KB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 2 - Forks: 1
lucianhu/Masterarbeit
Leveraging WES short reads for PAN-EXOME creation and analysis.
Language: WDL - Size: 18.6 MB - Last synced: 5 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
neherlab/pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
Language: Julia - Size: 35 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 75 - Forks: 6
gauravcodepro/pacbiohifi-read-assimilator
a pacbiohifi read check for the quick view of the read types.
Language: Shell - Size: 20.5 KB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 0
nf-core/pangenome
Renders a collection of sequences into a pangenome graph.
Language: Nextflow - Size: 4.16 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 49 - Forks: 14
gauravcodepro/pangenome-single-copy-gene
a single copy gene analysis pangenome which allows for the orthology already computed and allows for the alignment and phylogeny building using three alignment approaches and also allows for the GTRCAT and GTRGAMA model with 1000 bootstrap. To check the file conversion it iterates the first files at the start and see if the number matches
Language: Shell - Size: 18.6 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 1 - Forks: 0
gauravcodepro/streamlit-pangraphs-pangenome
a pangraph visualization and pangenome visualization component for the pangenome.
Language: Python - Size: 3.91 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 0
lh3/pangene
Constructing a pangenome gene graph
Language: C - Size: 595 KB - Last synced: 10 days ago - Pushed: 3 months ago - Stars: 132 - Forks: 6
gauravcodepro/pangenome-evolutionary
a complete workflow for analyzing the pangenomes from the core genesets. simply have to provide the fasta files and it will do everything and will make all the accessory information plots from the evolutionary analysis. It will also check for the breakage in the phylogeny and also will perform the repoint analysis.
Language: Shell - Size: 36.1 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 1 - Forks: 0
gauravcodepro/pangenome-proportion
a R function to estimate the proportion of the pangenome across the species after the orthology runs. It makes the proportion of the table across the species. You can provide the species file and then estimated
Language: R - Size: 25.4 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0
gauravcodepro/sra-explorer
a native enumaltor for the sra explorer and it will explore the sra and will bring all the information and will generate the go to files for the analysis. You simply have to provide as many as much as posisble SRA accessions for the use of the same.
Language: Shell - Size: 25.4 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0
gauravcodepro/panache-extract
maf to panache and extracting all snps and pangenome specific information.
Language: Ruby - Size: 48.8 KB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0
fpusan/SuperPang
Non-redundant pangenome assemblies from multiple genomes or bins
Language: Python - Size: 3.7 MB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 13 - Forks: 2
Tharos-ux/pancat
Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
Language: Python - Size: 1.74 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 28 - Forks: 1
maxgmarin/panqc
A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses
Language: Python - Size: 332 KB - Last synced: 19 days ago - Pushed: about 2 months ago - Stars: 13 - Forks: 0
longg2/LongBioinformatics
Scripts used by George S. Long
Language: Shell - Size: 349 KB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 1 - 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: 25 days ago - Pushed: 25 days ago - Stars: 4 - 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: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
labgem/PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
Language: Python - Size: 131 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 206 - Forks: 25
iferres/pagoo
A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
Language: R - Size: 38.7 MB - Last synced: 24 days ago - Pushed: over 1 year ago - Stars: 22 - Forks: 4
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: about 1 month ago - Pushed: 12 months ago - Stars: 42 - Forks: 4
heringerp/oxiqle Fork of oxigraph/oxigraph
SPARQL endpoint to represent pangenomic data
Language: HTML - Size: 5.61 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 1
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: 21 days ago - Pushed: 8 months ago - Stars: 39 - Forks: 7
eead-csic-compbio/get_homologues
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
Language: Perl - Size: 76.2 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 99 - Forks: 25
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
pg-space/panspace
Embedding-based indexing for compact storage, rapid querying, and curation of bacterial pan-genomes
Language: Jupyter Notebook - Size: 17.8 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - 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: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
JoshuaDanielRubin/SAFARI_data
Sensitive Alignments from a RYmer Index
Language: Python - Size: 1.24 GB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - 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: 2 months ago - Pushed: 2 months ago - Stars: 7 - Forks: 0
at-cg/PanAligner
Long read aligner for cyclic and acyclic pangenome graphs
Language: C - Size: 3.79 MB - Last synced: 3 months ago - Pushed: 5 months ago - Stars: 33 - Forks: 4
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: 6 months ago - Pushed: 6 months ago - Stars: 6 - Forks: 0
ouzounis/figshare
datasets shared on figshare
Size: 530 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0
pangenome/chromosome_communities
Recombination between heterologous human acrocentric chromosomes
Language: R - Size: 2.6 MB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 3 - Forks: 0
chmccarthy/Pangloss
Pangenome analysis of eukaryotes.
Language: Perl - Size: 21 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 15 - Forks: 4
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
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: 7 months ago - Pushed: 7 months ago - Stars: 21 - Forks: 5
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
nali321/Sequence2Branches
Sequence2Branches: Creating a species-level phylogenetic tree from paired FASTQ reads
Language: Python - Size: 120 KB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0
carleton-spacehogs/pangenome-selection
A repository as a Supplementary Methods of Moulana et al., 2019
Language: Python - Size: 5.04 MB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1
vjcitn/BiocHPRClk
A look at the pangenome consortium resources in AnVIL
Language: R - Size: 45 MB - Last synced: 7 days ago - Pushed: 10 months 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: 10 months ago - Pushed: about 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: 8 months ago - Pushed: about 2 years ago - Stars: 2 - 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: 10 months ago - Pushed: 10 months ago - Stars: 6 - Forks: 1
dcmonti/rs_graph_hash
Alignment (free) sequence to graph
Language: Rust - Size: 134 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
kevsilva/StrainFLAIR
Strain-level abundances estimation in metagenomic samples using variation graphs
Language: Python - Size: 75.2 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 24 - Forks: 5
AnimalGenomicsETH/bovine-graphs
Integrate multiple genome assemblies into a pangenome graph
Language: Python - Size: 23.4 MB - Last synced: about 1 year ago - Pushed: almost 2 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: about 1 year ago - Pushed: over 1 year 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: about 1 year ago - Pushed: over 1 year ago - Stars: 6 - Forks: 0
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: 8 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0
SioStef/panplots
A small R script for generating pangenome accumulation curves
Language: R - Size: 4.88 KB - Last synced: about 1 year ago - Pushed: about 2 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: 6 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0
iferres/simurg
Simulate pangenomes according to the IMG + Neutral models
Language: R - Size: 382 KB - Last synced: about 1 year ago - Pushed: almost 5 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: about 1 year ago - Pushed: over 1 year 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: about 1 year ago - Pushed: over 4 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: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 1
kloetzl/pangenomesim
♥ Simulate bacterial pangenomes.
Language: C++ - Size: 75.2 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 4 - Forks: 0
