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awesome-pangenomes

A list of software for pangenomics
https://github.com/colindaven/awesome-pangenomes

Last synced: 5 days ago
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A list of software capable of analyzing **eukaryotic** genomes for pangenomics
- GFA
- impg
- MoMI-G
- VAG
- Pancat
- PanSN-spec
- gfainject
- GRAFIMO - based Finding of Individual Motif Occurrences using vg
- rs-gfa
- PanKmer
- gfapy
- gfagraphs
- graphanalyzer
- GAM - Graph Alignment/Map - L54) Created by vg giraffe. May be superseded by GAF format.
- GAF - Graph Alignment Format
- Practical Pangenome Graphs
- graphanalyzer
A list of software capable of analyzing mainly **eukaryotic** genomes for pangenomics. A new section for microbial genomes has also been added, these tools may not scale to large genomes.
- Pantools v3+
- PHG Practical Haplotype Graph
- Deepvariant
- Pantera
- gaftools
- PATO
- Chrom_mini_graph
- MEMO
- poasta - affine sequence-to-graph and partial order aligner and MSA construction
- GraphAligner
- Hisat2
- GraphChainer
- Spades Pathracer
- Minichain
- PanAligner
- Paragraph - based genotyping tools for short read data
- Pangenie - based SV genotyping using short reads. Intended for human only (in 2023).
- GraphTyper
- SVarp
- Bandage
- SeqTubemap
- Panagram - mer conservation
- Panache
- Waragraph
- PanGraphViewer
- VRPG
- AGB
- graphgenomeviewer
- plotsr - generates static images
- nf-core pangenome
- Annotation_scripts - cactus pangenome with regions or SNPs
- Untangling-graphical-pangenomics - *important and frequently overlooked*
- PHI Pangenome-based Haplotype Inference
- pangepop - cactus and align reads against it with vg giraffe
- MGRgraph - genome Reference (warning - last updated 2018)
- impg
- vg validate
- odgi validate
- strangepg
- gfakluge
- gfatools
- gretl
- pgr-tk
- Minigraph
- minigraph_cactus
- PGGB
- pangene
- PSVCP
- GET_PANGENES
- bubblegun
- Wally
- Pantograph
- PGV
- gfaestus - accelerated using Vulkan
- gfaviz
- junctions - degenerate strings.
- rs-pancat-compare
- anvi'o - Annotation, Construction, Visualization and Manipulation (Eukaryote too excepted annotation)
- Roary - documented and feature-rich tool which works on Prokka gff files and has an entertaining FAQ.

Programming Languages

C++ 17 Python 13 Rust 9 C 7 JavaScript 3 TypeScript 2 Perl 1 Shell 1 Jupyter Notebook 1 Nextflow 1

Categories

A list of software capable of analyzing mainly **eukaryotic** genomes for pangenomics. A new section for microbial genomes has also been added, these tools may not scale to large genomes. 59 A list of software capable of analyzing **eukaryotic** genomes for pangenomics 17

Sub Categories

Keywords

bioinformatics 12 genomics 9 pangenome 9 variation-graph 7 pangenomics 6 genome-graph 4 pangenome-graph 4 variation-graphs 4 graphs 3 graph 2 machinelearning 2 visualization 2 graphs-algorithms 2 graphalignments 2 genomes 2 alignments 2 assembly 2 sequencing 2 alignment 2 sequence-alignment 2 gfa 2 long-reads 2 genome-variation-graphs 1 genomic-variants 1 vizualisation 1 javascript 1 structural-variants 1 haplotype-aware 1 graph-genome-browser 1 genome-browser 1 variants 1 genotype 1 genetics 1 decode-genetics 1 vcf 1 variant-calling 1 structural-variation 1 htslib 1 genotyping 1 read-alignment 1 read-aligners 1 read-mapping 1 graph-algorithms 1 pan-genome 1 contigs 1 mapping 1 plotting 1 sequencing-data 1 genomics-visualization 1 elastic-degenerate-string 1

Ecosyste.ms: Awesome

awesome-pangenomes

A list of software capable of analyzing eukaryotic genomes for pangenomics

A list of software capable of analyzing mainly eukaryotic genomes for pangenomics. A new section for microbial genomes has also been added, these tools may not scale to large genomes.