Correct misassemblies using Linked Reads

Split sequences at positions with low depth of coverage and high number of molecule starts.

Written by Shaun Jackman

Usage

To run Tigmint on the draft assembly assembly.fa with the reads reads.fq.gz, which have been run through longranger basic:

tigmint-make draft=myassembly reads=myreads

To run Tigmint and calculate assembly metrics using the reference genome GRCh38.fa:

tigmint-make draft=myassembly reads=myreads ref=GRCh38 G=3088269832

Note: tigmint-make is a Makefile script, and so any make options may also be used with tigmint-make, such as -n (--dry-run).

Parameters of Tigmint

• draft: Name of the draft assembly, draft.fa
• reads: Name of the reads, reads.fq.gz
• depth_threshold=100: Depth of coverage threshold
• starts_threshold=4: Number of molecule starts threshold
• minsize=2000: Minimum molecule size
• as=100: Minimum alignment score
• nm=5: Maximum number of mismatches
• t=8: Number of threads
• gzip=gzip: gzip compression program, use pigz -p8 for parallelized compression

Parameters of ARCS

• c=5
• e=30000
• r=0.05

Parameters of LINKS

• a=0.1
• l=10

Parameters for calculating assembly metrics

• ref: Reference genome, ref.fa, for calculating assembly contiguity metrics
• G: Size of the reference genome, for calculating NG50 and NGA50