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tigmint

⛓ Correct misassemblies using linked reads

Correct misassemblies using Linked Reads

Split sequences at positions with a low number of spanning molecules

Written by Shaun Jackman.

Description

Tigmint identifies and corrects misassemblies using linked reads from 10x Genomics Chromium. The reads are first aligned to the assembly, and the extents of the large DNA molecules are inferred from the alignments of the reads. The physical coverage of the large molecules is more consistent and less prone to coverage dropouts than that of the short read sequencing data. Each scaffold is scanned with a fixed window to identify areas where there are few spanning molecules, revealing possible misassemblies. Scaffolds are cut where spanning molecules are identified following windows with no spanning molecules.

Installation

Download and extract the source code. Compiling is not needed.

git clone https://github.com/bcgsc/tigmint && cd tigmint

or

curl -L https://github.com/bcgsc/tigmint/archive/master.tar.gz | tar xz && mv tigmint-master tigmint && cd tigmint

Dependencies

Python package dependencies

pip3 install intervaltree pybedtools pysam statistics

Tigmint uses Bedtools, BWA and Samtools. These dependencies may be installed using Homebrew on macOS or Linuxbrew on Linux.

Install the dependencies of Tigmint

brew install bedtools bwa samtools

Install the dependencies of ARCS (optional)

brew install arcs links-scaffolder

Install the dependencies for calculating assembly metrics (optional)

brew install abyss seqtk

Usage

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

tigmint tigmint draft=myassembly reads=myreads

To run both Tigmint and scaffold the corrected assembly with ARCS:

tigmint arcs draft=myassembly reads=myreads

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

tigmint metrics draft=myassembly reads=myreads ref=GRCh38 G=3088269832

Note

Commands

Parameters of Tigmint

Parameters of ARCS

Parameters of LINKS

Parameters for calculating assembly metrics

Tips

Support

After first looking for existing issue at https://github.com/bcgsc/tigmint/issues, please report a new issue at https://github.com/bcgsc/tigmint/issues/new. Please report the names of your input files, the exact command line that you are using, and the entire output of tigmint.

Pipeline

Tigmint pipeline illustration

Makefile · CWL · CWLViewer

Tigmint pipeline Makefile