Nextflow Modules
Showing module(s) with keyword "gfa"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bandage/image | Process | gfa graph assembly visualisation | Render an assembly graph in GFA 1.0 format to PNG and SVG image formats |
| nf-core/dnaapler/all | Process | reorientation genome assembly chromosome plasmid phage dnaA fasta gfa | Reorients complete bacterial chromosomes, plasmids and phages to start at a conserved gene |
| nf-core/dshbio/exportsegments | Process | gfa assembly segment | Export assembly segment sequences in GFA 1.0 format to FASTA format |
| nf-core/gfaffix | Process | gfa graph pangenome variation graph | Collapse walk-preserving shared affixes in variation graphs in GFA format |
| nf-core/gfatools/gfa2fa | Process | gfa rgfa fasta assembly genome graph genomics | Converts GFA or rGFA files to FASTA |
| nf-core/gfatools/stat | Process | summary statistics gfa rgfa graph genomics | Summary statistics for GFA files |
| nf-core/odgi/build | Process | variation graph pangenome graph gfa graph construction | Construct a dynamic succinct variation graph in ODGI format from a GFAv1. |
| nf-core/odgi/draw | Process | variation graph pangenome graph gfa graph drawing | Draw previously-determined 2D layouts of the graph with diverse annotations. |
| nf-core/odgi/layout | Process | variation graph pangenome graph gfa graph layout | Establish 2D layouts of the graph using path-guided stochastic gradient descent. The graph must be sorted and id-compacted. |
| nf-core/odgi/sort | Process | variation graph pangenome graph gfa graph layout | Apply different kind of sorting algorithms to a graph. The most prominent one is the PG-SGD sorting algorithm. |
| nf-core/odgi/squeeze | Process | squeeze odgi gfa combine graphs | Squeezes multiple graphs in ODGI format into the same file in ODGI format. |
| nf-core/odgi/stats | Process | variation graph pangenome graph gfa graph stats | Metrics describing a variation graph and its path relationship. |
| nf-core/odgi/unchop | Process | variation graph pangenome graph gfa graph unchopping | Merge unitigs into a single node preserving the node order. |
| nf-core/odgi/view | Process | variation graph pangenome graph gfa graph formats | Project a graph into other formats. |
| nf-core/odgi/viz | Process | variation graph pangenome graph gfa graph viz | Visualize a variation graph in 1D. |
| nf-core/panacus/histgrowth | Process | statistics pangenome graph gfa genomics | Calculates a coverage histogram from a GFA file and constructs a growth table from this as either a TSV or HTML file |
| nf-core/seqwish/induce | Process | induce paf gfa graph variation graph | Induce a variation graph in GFA format from alignments in PAF format |
| nf-core/smoothxg | Process | gfa graph pangenome variation graph POA | Linearize and simplify variation graph in GFA format using bloc |