View on GitHub

tigmint

⛓ Correct misassemblies using linked reads

Correct misassemblies using Linked Reads

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

Written by Shaun Jackman.

Poster and slides HTML · PDF · Markdown

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. Atypical drops in physical molecule coverage, less than the median minus two times the inter-quartile range, reveal possible misassemblies. Clipped alignments of the first and last reads of a molecule are used to refine the coordinates of the misassembly with base-pair accuracy.

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

Dependencies may be installed using Homebrew on macOS or Linuxbrew on Linux.

Install the dependencies of Tigmint

brew tap homebrew/science
brew install bedtools bwa gawk gnu-sed miller pigz r samtools seqtk
Rscript -e 'install.packages(c("ggplot2", "rmarkdown", "tidyverse", "uniqtag"))'

Install the dependencies of ARCS (optional)

brew install arcs links-scaffolder

Install the dependencies for calculating assembly metrics (optional)

brew install abyss

Usage

Change your current working directory to the directory in which Tigmint is installed: cd tigmint

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

tigmint-make tigmint draft=myassembly reads=myreads

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

tigmint-make arcs draft=myassembly reads=myreads

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

tigmint-make 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

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-make.

Pipeline

Makefile · CWL · CWLViewer

Tigmint pipeline