Strainline

Description

Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read data, or collapse haplotype-specific variations into consensus sequence. Here, we present Strainline, a novel approach to assemble viral haplotypes from noisy long reads without a reference genome. As a crucial consequence, Strainline is the first approach to provide strain-resolved, full-length de novo assemblies of viral quasispecies from noisy third-generation sequencing data. Benchmarking experiments on both simulated and real datasets of varying complexity and diversity confirm this novelty, by demonstrating the superiority of Strainline in terms of relevant criteria in comparison with the state of the art.

Installation and dependencies

Strainline relies on the following dependencies:

minimap2
daccord
samtools
spoa
jgi_summarize_bam_contig_depths program from metabat2
Python v3.6+

To run Strainline, firstly, it is recommended to install the dependencies through Conda. Also, DAZZ_DB and DALIGNER are required before running daccord.

conda create -n strainline
conda activate strainline
conda install -c bioconda minimap2 spoa samtools dazz_db daligner metabat2

Then, one could just download executable program and link daccord to the /path/to/envs/strainline/bin/. Change the /path/to/ as your own path to conda. Make sure that daccord -h can work successfully.

wget https://github.com/gt1/daccord/releases/download/0.0.10-release-20170526170720/daccord-0.0.10-release-20170526170720-x86_64-etch-linux-gnu.tar.gz
tar -zvxf daccord-0.0.10-release-20170526170720-x86_64-etch-linux-gnu.tar.gz 
ln -fs $PWD/daccord-0.0.10-release-20170526170720-x86_64-etch-linux-gnu/bin/daccord /path/to/envs/strainline/bin/daccord

You can also install with docker directly, please see the end.

Running and options

The input read file is required and the format should be FASTA. Other parameters are optional. Please run strainline.sh -h to get details of optional parameters setting. Before running Strainline, please read through the following basic parameter settings, which may be helpful to achieve better assemblies.

Usage: strainline.sh [options] -i reads.fasta -o out -p sequencingPlatform

Input:
    reads.fasta:                      fasta file of input long reads.
    out:                             directory where to output the results.
    sequencingPlatform:               long read sequencing platform: PacBio (-p pb) or Oxford Nanopore (-p ont)

Options:
    --minTrimmedLen INT:              Minimum trimmed read length. (default: 1000)
    --topk INT, -k INT:               Choose top k seed reads. (default: 50)
    --minOvlpLen INT:                 Minimum read overlap length. (default: 1000)
    --minIdentity FLOAT:              Minimum identity of overlaps. (default: 0.99)
    --minSeedLen INT:                 Minimum seed read length. (default: 3000)
    --maxOH INT:                      Maximum overhang length allowed for overlaps. (default: 30)
    --iter INT:                       Number of iterations for contig extension. (default: 2)
    --maxGD FLOAT:                    Maximum global divergence allowed for merging haplotypes. (default: 0.01)
    --maxLD FLOAT:                    Maximum local divergence allowed for merging haplotypes. (default: 0.001)
    --maxCO INT:                      Maximum overhang length allowed for contig contains. (default: 5)
    --minAbun FLOAT:                  Minimum abundance for filtering haplotypes (default: 0.02)
    --rmMisassembly BOOL:             Break contigs at potential misassembled positions (default: False)
    --correctErr BOOL:                Perform error correction for input reads (default: True)
    --threads INT, -t INT:            Number of processes to run in parallel (default: 8).
    --help, -h:                       Print this help message.

Examples

One can test the strainline.sh program using the small PacBio CLR reads file example/reads.fa. Please use the absolute path of strainline.sh when running the program.

PacBio CLR reads

cd example
/abspath/Strainline/src/strainline.sh -i reads.fa -o out -p pb -k 20 -t 32

ONT reads

/abspath/Strainline/src/strainline.sh -i reads.fa -o out -p ont -t 32

Installation with docker and example test

git clone https://github.com/HaploKit/Strainline.git
cd Strainline/docker
docker build -t strainline .

cd ../example

# 1. run directly in your path with data
docker run -v $PWD:$PWD -w $PWD strainline strainline.sh -i reads.fa -o out -p pb -k 20 -t 16
# 2. start an interactive docker container session and run in your path with data
docker run -it --rm -v $PWD:/wd -w /wd -v /var/run/docker.sock:/var/run/docker.sock strainline /bin/bash
strainline.sh -i reads.fa -o out -p pb -k 20 -t 16

Citation

Luo, X., Kang, X. & Schönhuth, A. Strainline: full-length de novo viral haplotype reconstruction from noisy long reads. Genome Biol 23, 29 (2022). https://doi.org/10.1186/s13059-021-02587-6

HaploKit / Strainline

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