aafshinfard/ntLink

Scaffolding genome assemblies using long reads and minimizers

Description of the algorithm

ntLink uses minimizers to perform a lightweight mapping between the input target assembly and the supplied long reads. These long-read mappings are then used as evidence to orient and order the output scaffolds.

General steps in the algorithm:

Compute ordered minimizer sketches of the input target assembly and long reads
Use minimizers to map the long reads to the target assembly contigs
Find contig pairs, where joins are suggested by the long-read mapping evidence
Output a scaffold graph, where the nodes are oriented contigs and the edges are joins suggested by the long read data
Traverse the scaffold graph using abyss-scaffold to output the final scaffolds

Credits

Concept: Rene Warren and Lauren Coombe

Design and implementation: Lauren Coombe

Citing ntLink

If you use ntLink in your research, please cite:

Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL and Birol I. LongStitch: high-quality genome assembly correction and scaffolding using long reads. BMC Bioinformatics 22, 534 (2021). https://doi.org/10.1186/s12859-021-04451-7

Usage

ntLink: Scaffolding assemblies using long reads
Usage: ntLink scaffold target=<target scaffolds> reads='List of long read files'

To additionally run gap-filling (fill gap regions with raw read sequence):
Usage: ntLink scaffold gap_fill target=<target scaffolds> reads='List of long read files'

Options:
target			Target assembly to be scaffolded in fasta format
reads		        List of long read files (separated by a space)
prefix			Prefix of intermediate output files [<target>.k<k>.w<w>.n<n>]
t			Number of threads [4]
k			K-mer size for minimizers [32]
w			Window size for minimizers [100]
n			Minimum graph edge weight [1]
g			Minimum gap size (bp) [20]
f			Maximum number of contigs in a run for full transitive edge addition [10]
a                       Minimum number of anchored ONT reads required for an edge [1]
z			Minimum size of contig (bp) to scaffold [1000]
v                       If 1, track time and memory for each step of the pipeline [0]
conservative		If False, runs ntLink in stitching mode [True]
overlap			If True, runs extra step to attempt to identify and trim overlapping joined sequences [True]

Note: 
	- Ensure all assembly and read files are in the current working directory, making soft links if necessary

Running ntLink help prints the help documentation.

Input reads files can be gzipped (or not), and in either fastq or fasta format

Example

Input files:

target assembly my_assembly.fa
long read file long_reads.fq.gz

ntLink command:

ntLink scaffold target=my_assembly.fa reads=long_reads.fq.gz k=32 w=250

The post-ntLink scaffolds file will have the suffix *ntLink.scaffolds.fa

Gap-filling

As of ntLink v1.2.0, ntLink can also run gap-filling after the scaffolding stage. This mode is enabled by adding the gap_fill target to the ntLink command. overlap=True is required when using the gap_fill feature.

Note that the gaps will be filled with raw read sequence, so subsequent polishing is a good idea. See the wiki page for more details.

For more information about the ntLink algorithm and tips for running ntLink see our wiki

Installation

ntLink is available from conda and homebrew package managers.

Installing using conda:

conda install -c bioconda -c conda-forge ntlink

Installing using brew:

brew install brewsci/bio/ntlink

Installing from source code:

git clone https://github.com/bcgsc/ntLink.git
cd src
make

Testing your installation

To test your ntLink installation:

cd tests
./test_installation.sh

The expected output files can be found in: tests/expected_outputs

Dependencies

Python3 (Numpy, Python-igraph)
ABySS v2.3.0+
GCC 5+ or Clang 4+ with OpenMP
zlib

Python dependencies can be installed with:

pip3 install -r requirements.txt

License

ntLink is released under the GNU General Public License v3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, version 3.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

For commercial licensing options, please contact Patrick Rebstein (prebstein@bccancer.bc.ca).

aafshinfard / ntLink