Description

"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)"

Input

Name
Description
Pattern

0 ()

1 ()

0 ()

1 ()

0 ()

0 ()

0 ()

0 ()

Output

Name
Description
Pattern

scaffold_dot ()

arcs_tsv ()

arcs_gv ()

arcs_checkpoint_tsv ()

arcs_scaffolds_fa ()

arcs_scaffolds_renamed ()

abyss_scaffolds_fa ()

stitch_path ()

trimmed_scaffolds_agp ()

trimmed_scaffolds_fasta ()

trimmed_scaffolds_path ()

trimmed_scaffolds_tsv ()

verbose_mapping_tsv ()

tsv ()

versions ()

Tools

longstitch Documentation

A genome assembly correction and scaffolding pipeline using long reads

doi: 10.1186/s12859-021-04451-7License: GPL v3-or-later, GPL v3
Authors