×

nf-core/longstitch @ 0.0.0-6c4ed3a

"A genome assembly correction and scaffolding pipeline using long reads, consisting of up to three steps:

  • Tigmint cuts the draft assembly at potentially misassembled regions
  • ntLink is then used to scaffold the corrected assembly
  • followed by ARKS for further scaffolding (optional)"
scaffolding long read assembly correction
Latest version: 0.0.0-6c4ed3a
Total downloads: 10
Source: nf-core/modules
Authors: @nschan
Maintainers: @nschan

Summary

"A genome assembly correction and scaffolding pipeline using long reads, consisting of up to three steps:

  • Tigmint cuts the draft assembly at potentially misassembled regions
  • ntLink is then used to scaffold the corrected assembly
  • followed by ARKS for further scaffolding (optional)"

Get started

Add the following snippet to your workflow script to include this module.

include { LONGSTITCH } from 'nf-core/longstitch'

License

MIT License

Process
Name LONGSTITCH
Input 6 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
assembly file

Draft assembly

 *.{fa,fasta,fa.gz,fasta.gz}
#2 tuple
meta2 map

Groovy Map containing sample information e.g. [ id:'sample1' ]
reads file

long reads

 *.{fq,fastq,fq.gz,fastq.gz}
command string

Longstitch command to run. Valid options are: ["run", "tigmint-ntLink-arks", "tigmint-ntLink", "ntLink-arks"]
span string

min number of spanning molecules to be considered correctly assembled. Either span or genomesize need to be provided.
genomesize string

Expected genome size. Either span or genomesize need to be provided.
longmap string

Type of long-read (passed to minimap2). Valid options are: [ "ont", "pb", "hifi" ]
Output 25 channels
#1 tsv tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*.k*.w???.tsv file

scaffolding tsv file

 *.k*.w???.tsv
#2 arcs_gv tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*k*.w*.z*.ntLink.scaffolds_*_original.gv file

arcs graph

 *k*.w*.z*.ntLink.scaffolds_*_original.gv
#3 arcs_tsv tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*k*.w*.z*.ntLink.scaffolds_*_main.tsv file

arcs tsv file

 *k*.w*.z*.ntLink.scaffolds_*_main.tsv
#4 links_gv tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*k*.w*.z*.ntLink.scaffolds_*_l*.gv file

Links graph

 *k*.w*.z*.ntLink.scaffolds_*_l*.gv
#5 versions
versions.yml file

File containing software versions

 versions.yml
#6 links_log tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*k*.w*.z*.ntLink.scaffolds_*_l*.log file

Links logfile

 *k*.w*.z*.ntLink.scaffolds_*_l*.log
#7 stitch_path tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*k*.w*.z*.stitch.path file

stitch paths

 *k*.w*.z*.stitch.path
#8 scaffold_dot tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*k*.w*.z*.n*.scaffold.dot file

Scaffold dot file

 *k*.w*.z*.n*.scaffold.dot
#9 links_scaffolds tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]