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⛓ Correct misassemblies using linked AND long reads

Release Conda Issues

Correct misassemblies in genome assembly drafts using linked or long sequencing reads

Cut sequences at positions with few spanning molecules.

Written by Shaun Jackman, Lauren Coombe, Justin Chu, and Janet Li.

Paper · Slides · Poster


Shaun D. Jackman, Lauren Coombe, Justin Chu, Rene L. Warren, Benjamin P. Vandervalk, Sarah Yeo, Zhuyi Xue, Hamid Mohamadi, Joerg Bohlmann, Steven J.M. Jones and Inanc Birol (2018). Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinformatics, 19(1). doi:10.1186/s12859-018-2425-6


Tigmint identifies and corrects misassemblies using linked (e.g. MGI’s stLFR, 10x Genomics Chromium) or long (e.g. Oxford Nanopore Technologies long reads) DNA sequencing reads. 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. The sequences are cut at positions that have insufficient spanning molecules. Tigmint outputs a BED file of these cut points, and a FASTA file of the cut sequences.

Tigmint also allows the use of long reads from Oxford Nanopore Technologies. The long reads are segmented and assigned barcodes, and the following steps of the pipeline are the same as described above.

Each window of a specified fixed size is checked for a minimum number of spanning molecules. Sequences are cut at those positions where a window with sufficient coverage is followed by some number of windows with insufficient coverage is then followed again by a window with sufficient coverage.


Install Tigmint using Brew

brew install tigmint

Install Tigmint using Conda

conda install -c bioconda -c conda-forge tigmint

Run Tigmint using Docker

docker run

Install Tigmint from the source code

Download and extract the source code.

git clone && cd tigmint
make -C src


curl -L | tar xz && cd tigmint-1.2.10
make -C src


Install Python package dependencies

conda install -c bioconda intervaltree pybedtools pysam numpy bedtools minimap2 bwa zsh btllib samtools

Install the dependencies of ARCS (optional)

conda install -c bioconda arcs links

Install the dependencies for calculating assembly metrics (optional)

conda install -c bioconda abyss seqtk


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

To run Tigmint with long reads in fasta or fastq format (myreads.fa.gz or myreads.fq.gz - or uncompressed) on the draft assembly myassembly.fa for an organism with a genome size of gsize:

tigmint-make tigmint-long draft=myassembly reads=myreads span=auto G=gsize dist=auto

Optionally, ntLink (v1.3.6+) can be used to map the long reads to the draft assembly. To use ntLink mappings, specify mapping=ntLink to your tigmint command.


tigmint-make commands

Parameters of Tigmint

Parameters of ARCS

Parameters of LINKS

Parameters for calculating assembly metrics


Using stLFR linked reads

To use stLFR linked reads with Tigmint, you will need to re-format the reads to have the barcode in a BX:Z: tag in the read header. For example, this format

@V100002302L1C001R017000000#0_0_0/1 0	1

should be changed to:

@V100002302L1C001R017000000 BX:Z:0_0_0


After first looking for an existing issue at, please report a new issue at Please report the names of your input files, the exact command line that you are using, and the entire output of Tigmint.


Tigmint pipeline illustration