Topic: pangenome Goto Github
Some thing interesting about pangenome
Some thing interesting about pangenome
pangenome,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).
User: 444thliao
pangenome,Integrate multiple genome assemblies into a pangenome graph
Organization: animalgenomicseth
pangenome,Long read aligner for cyclic and acyclic pangenome graphs
Organization: at-cg
pangenome,Archive of personal scripts repository from my various projects in the Buell Lab at MSU (Jan. 2008 - Apr. 2011)
User: brettwhitty
pangenome,Pangenome analysis of eukaryotes.
User: chmccarthy
pangenome,Développement des outils informatiques pour l'analyse de données - Projet porté par Guillame GAUTREAU - INRAE
Organization: d4gen-genopole
pangenome,Integrate multiple assemblies into a pangenome graph
User: danangcrysnanto
pangenome,My PhD dissertation on bovine pangenome graph
User: danangcrysnanto
pangenome,GET_HOMOLOGUES: a versatile software package for pan-genome analysis
User: eead-csic-compbio
pangenome,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.
User: farhanariaz123
pangenome,Non-redundant pangenome assemblies from multiple genomes or bins
User: fpusan
pangenome,Space-efficient minimizer-based pangenome reference graph and haplotype mapping tool
User: gaojunxuan
pangenome,Single Cell guided Pangenome analysis pipeline using SPAdes, CheckM, GTDB-Tk, Prokka, Roary and extensive quality control.
User: gongyh
Home Page: https://nf-co.re/scp
pangenome,A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
User: iferres
Home Page: https://iferres.github.io/pagoo/
pangenome,Simulate pangenomes according to the IMG + Neutral models
User: iferres
pangenome,Pangenome clustering using entropy, relative entropy, cumulative RE, hybrid distributions, et.al
User: jsa-aerial
pangenome,Strain-level abundances estimation in metagenomic samples using variation graphs
User: kevsilva
pangenome,♥ Simulate bacterial pangenomes.
User: kloetzl
pangenome,Build a partitioned pangenome graph from microbial genomes
Organization: labgem
Home Page: https://ppanggolin.readthedocs.io/en/latest/
pangenome,Scripts used by George S. Long
User: longg2
pangenome,Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-mers. bioRxiv. (2023).
User: lucaparmigiani
Home Page: https://doi.org/10.1101/2022.11.15.516472
pangenome,Leveraging WES short reads for PAN-EXOME creation and analysis.
User: lucianhunguyen
pangenome,Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
Organization: marschall-lab
pangenome,A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses
User: maxgmarin
Home Page: https://pypi.org/project/panqc/
pangenome,PAPi (Pangenome Analysis Pipeline)
User: michkam89
pangenome,Extract flexible bacterial core genome alignments and compute SNP distances. Additionally, perform rarefaction-sampling analysis of alignments
User: moorembioinfo
pangenome,Sequence2Branches: Creating a species-level phylogenetic tree from paired FASTQ reads
User: nali321
pangenome,A bioinformatic toolkit to align genome assemblies into pangenome graphs
Organization: neherlab
Home Page: https://neherlab.github.io/pangraph
pangenome,datasets shared on figshare
User: ouzounis
Home Page: https://github.com/ouzounis/figshare
pangenome,Recombination between heterologous human acrocentric chromosomes
Organization: pangenome
Home Page: https://doi.org/10.1038/s41586-023-05976-y
pangenome,ODGI: understanding pangenome graphs (https://doi.org/10.1093/bioinformatics/btac308)
Organization: pangenome
pangenome,Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)
User: rx32940
pangenome,a pacbiohifi read check for the quick view of the read types and making it easy for the fasta manipulations and read extractions. You can spawn also this in rust.
User: sablokgaurav
pangenome,maf to panache and extracting all snps and pangenome specific information.
User: sablokgaurav
pangenome,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.
User: sablokgaurav
pangenome,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
User: sablokgaurav
pangenome,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.
User: sablokgaurav
pangenome,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.
Organization: salvadorlab
pangenome,PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
Organization: segatalab
pangenome,A small R script for generating pangenome accumulation curves
User: siostef
pangenome,Workflow to construct linear representation of pan genome from deep WGS data and public assemblies
User: songtaogui
pangenome,the miscellaneous analysis scripts used in the research of pan-Zea genome and genetics
User: songtaogui
pangenome,Structure variants calling and genotyping scripts for pan-Zea
User: songtaogui
pangenome,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.
Organization: southgreenplatform
pangenome,Library to parse, edit and handle in memory GFA graphs
User: tharos-ux
Home Page: https://tharos-ux.github.io/pangenome-notes/
pangenome,Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions
User: tharos-ux
Home Page: https://tharos-ux.github.io/pangenome-notes/
pangenome,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.
Organization: upobioinfo
pangenome,A look at the pangenome consortium resources in AnVIL
User: vjcitn
Home Page: https://vjcitn.github.io/BiocHPRClk/
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