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awesome-pangenomes
A list of software for pangenomics
https://github.com/colindaven/awesome-pangenomes
Last synced: 11 minutes ago
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A list of software capable of analyzing **eukaryotic** genomes for pangenomics
- Pantograph
- GFA
- Pantools v3+
- PHG Practical Haplotype Graph
- GET_PANGENES
- Deepvariant
- gfatools
- gfakluge
- gaftools
- gretl
- pgr-tk
- Minigraph
- minigraph_cactus
- PGGB
- pangene
- PSVCP
- PATO
- Chrom_mini_graph
- impg
- 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
- bubblegun
- Bandage
- SeqTubemap
- MoMI-G
- Panagram - mer conservation
- VAG
- Panache
- Waragraph
- PanGraphViewer
- Wally
- VRPG
- PGV
- Pancat
- gfaestus - accelerated using Vulkan
- gfaviz
- AGB
- pangenome - core Nextflow pipeline using PGGB and odgi components. Better parallelized than PGGB alone. :rocket:
- PanSN-spec
- gfainject
- GRAFIMO - based Finding of Individual Motif Occurrences using vg
- rs-gfa
- PanKmer
- gfapy
- gfagraphs
- graphanalyzer
- graphgenomeviewer
- plotsr - generates static images
- GAM - Graph Alignment/Map - L54) Created by vg giraffe. May be superseded by GAF format.
- GAF - Graph Alignment Format
- Practical Pangenome Graphs
- graphanalyzer
- MoMI-G
- VAG
- odgi validate
- Untangling-graphical-pangenomics - *important and frequently overlooked*
- pangepop - cactus and align reads against it with vg giraffe
- MGRgraph - genome Reference (warning - last updated 2018)
- vg validate
Programming Languages
Sub Categories
Keywords
bioinformatics
11
genomics
8
pangenome
7
variation-graph
6
genome-graph
4
pangenomics
4
variation-graphs
3
graphs
3
graph
2
assembly
2
alignment
2
long-reads
2
pangenome-graph
2
machinelearning
2
graphs-algorithms
2
graphalignments
2
genomes
2
alignments
2
gfa
2
sequence-alignment
2
graph-representation
1
read-mapping
1
read-aligners
1
graph-algorithms
1
parsing
1
r
1
read-alignment
1
pan-genome
1
genotyping
1
htslib
1
structural-variation
1
variant-calling
1
vcf
1
decode-genetics
1
dna
1
sequence-analysis
1
motif-scanning
1
haplotype-aware
1
genomic-variants
1
genome-variation-graphs
1
workflow
1
pipeline
1
nf-core
1
nextflow
1
genomics-visualization
1
visualization
1
sequencing-data
1
sequencing
1
plotting
1
mapping
1