Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
awesome-pangenomes
A list of software for pangenomics
https://github.com/colindaven/awesome-pangenomes
- vg - Formats#gam-graph-alignment--map-vgs-bam
- odgi
- gfatools
- gfakluge
- gaftools
- gretl
- pgr-tk
- Minigraph
- Cactus/minigraph
- PGGB
- Pantools v3+
- PSVCP
- PHG Practical Haplotype Graph
- PATO
- Chrom_mini_graph
- GET_PANGENES
- impg
- MGRgraph - genome Reference (warning - last updated 2018)
- pangene
- MEMO
- poasta - affine sequence-to-graph and partial order aligner and MSA construction
- vg map
- vg giraffe
- Hisat2
- Minigraph
- Chrom_mini_graph
- GraphAligner
- Minigraph
- GraphChainer
- Spades Pathracer
- Minichain
- PanAligner
- poasta - affine sequence-to-graph and partial order aligner and MSA construction
- vg call
- Paragraph - based genotyping tools for short read data
- Pangenie - based SV genotyping using short reads. Intended for human only (in 2023).
- vg surject
- Deepvariant
- vg call
- GraphTyper
- Pangenie - based SV genotyping using short reads. Intended for human only (in 2023).
- SVarp
- bubblegun
- Panagram
- Bandage
- SeqTubemap
- VAG
- Panache
- Waragraph
- PanGraphViewer
- Wally
- VRPG
- Pantograph
- PGV
- Pancat
- gfaestus - accelerated using Vulkan
- gfaviz
- AGB
- MoMI-G
- pangene
- vg view - generates static images
- odgi
- pangenome - core Nextflow pipeline using PGGB and odgi components. Better parallelized than PGGB alone. :rocket:
- pangepop - cactus and align reads against it with vg giraffe
- vg validate
- odgi validate
- GFA
- rGFA
- vg - Formats#gam-graph-alignment--map-vgs-bam
- odgi
- PanSN-spec
- GAF - Graph Alignment Format
- GAM - Graph Alignment/Map - L54) Created by vg giraffe. May be superseded by GAF format.
- gfainject
- GRAFIMO - based Finding of Individual Motif Occurrences using vg
- rs-gfa
- PanKmer
- gfapy
- gfagraphs
- graphanalyzer
- Practical Pangenome Graphs
Programming Languages
Keywords
bioinformatics
10
genomics
8
pangenome
7
variation-graph
5
pangenomics
4
variation-graphs
3
genome-graph
3
sequence-alignment
2
alignment
2
assembly
2
gfa
2
long-reads
2
graph
2
graphs
2
pangenome-graph
2
genome-variation-graphs
1
genomic-variants
1
haplotype-aware
1
motif-scanning
1
graph-representation
1
parsing
1
genomics-visualization
1
visualization
1
sequencing-data
1
sequencing
1
plotting
1
mapping
1
contigs
1
vizualisation
1
javascript
1
dna
1
vcf
1
variant-calling
1
structural-variation
1
htslib
1
genotyping
1
workflow
1
pipeline
1
nf-core
1
nextflow
1
machinelearning
1
graphs-algorithms
1
graphalignments
1
genomes
1
alignments
1
sequence-analysis
1
variants
1
genotype
1
genetics
1
decode-genetics
1