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

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Description
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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

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Description
Pattern

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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