Wengan demo
September 28, 2020 ยท View on GitHub
This repository contains a test dataset and the instructions to run Wengan (version 0.2).
Table of Contents
Download the Wengan code
This test uses the precompiled binaries of Wengan (v0.2). The Linux precompiled binaries can be downloaded using the following command:
wget https://github.com/adigenova/wengan/releases/download/v0.2/wengan-v0.2-bin-Linux.tar.gz
tar zxvf wengan-v0.2-bin-Linux.tar.gz
# set WG to
export WG=$PWD/wengan-v0.2-bin-Linux/wengan.pl
Running the E.coli demo
Dataset description
| Technology | # of reads | Genome coverage | Description | Files | Source |
|---|---|---|---|---|---|
| Illumina | 415,598 | 50 | 2 x 300 bp | EC.50X.R1.fastq.gz EC.50X.R2.fastq.gz | Schatz Lab |
| Nanopore | 3,116 | 30 | N50: 46kb | EC.ONT.30X.fa.gz | Loman lab |
| PacBio | 9,369 | 30 | N50: 17kb | EC.PAC.30X.fa.gz | PacBio website |
The original datasets are available at the listed sources. We subsampled the original files to the listed genome coverage.
Hardware used
This test was run in a node of the cluster leftraru (NLHPC Chile). The node has the following hardware and software:
- CPUs : Intel(R) Xeon(R) Gold 6152 CPU @ 2.10GHz (44 threads).
- RAM : 188 Gb RAM.
- File System : Lustre (EXAScaler)
- Operating system : Linux 3.10.0-862.14.4.el7.x86_64
Wengan commands
Running WenganD
#WG should point to wengan.pl script (found in the root installation directory)
WG=$PATH_TO/wengan-v0.2-bin-Linux/wengan.pl
# Assembling Illumina + Nanopore reads
perl ${WG} -x ontraw -a D -s ecoli/reads/EC.50X.R1.fastq.gz,ecoli/reads/EC.50X.R2.fastq.gz -l ecoli/reads/EC.ONT.30X.fa.gz -p ec_Wd_or1 -t 10 -g 5
# Assembling Illumina + PacBio (CLR) reads
perl ${WG} -x pacraw -a D -s ecoli/reads/EC.50X.R1.fastq.gz,ecoli/reads/EC.50X.R2.fastq.gz -l ecoli/reads/EC.PAC.30X.fa.gz -p ec_Wd_pr1 -t 10 -g 5
Expected results
The fasta file *.SPolished.asm.wengan.fasta (ec_Wd_or1.SPolished.asm.wengan.fasta and ec_Wd_pr1.SPolished.asm.wengan.fasta respectively) contains the final genome assembly reported by Wengan. Both hybrid datasets are assembled to a single contig sequence (Genome Size of ~4.6 Mb).
Computational resources
The expected runtime with a single core is about 10 minutes and with 10 cores about 2 Minutes. The maximum RAM usage is around ~9 Gb.
Running WenganA
#WG should point to wengan.pl script (found in the root installation directory)
WG=$PATH_TO/wengan-v0.2-bin-Linux/wengan.pl
# Assembling Illumina + Nanopore reads
perl ${WG} -x ontraw -a A -s ecoli/reads/EC.50X.R1.fastq.gz,ecoli/reads/EC.50X.R2.fastq.gz -l ecoli/reads/EC.ONT.30X.fa.gz -p ec_Wa_or1 -t 10 -g 5
# Assembling Illumina + PacBio (CLR) reads
perl ${WG} -x pacraw -a A -s ecoli/reads/EC.50X.R1.fastq.gz,ecoli/reads/EC.50X.R2.fastq.gz -l ecoli/reads/EC.PAC.30X.fa.gz -p ec_Wa_pr1 -t 10 -g 5
Expected results
The fasta file *.SPolished.asm.wengan.fasta (ec_Wa_or1.SPolished.asm.wengan.fasta and ec_Wa_pr1.SPolished.asm.wengan.fasta respectively) contains the final genome assembly reported by Wengan. Both hybrid datasets are assembled to a single contig sequence (Genome Size of ~4.6 Mb).
Computational resources
The expected runtime with a single core is about 10 minutes and with 10 cores about 2 Minutes. The maximum RAM usage is around ~4 Gb.
Running WenganM
#WG should point to wengan.pl script (found in the root installation directory)
WG=$PATH_TO/wengan-v0.2-bin-Linux/wengan.pl
# Assembling Illumina + Nanopore reads
perl ${WG} -x ontraw -a M -s ecoli/reads/EC.50X.R1.fastq.gz,ecoli/reads/EC.50X.R2.fastq.gz -l ecoli/reads/EC.ONT.30X.fa.gz -p ec_Wm_or1 -t 10 -g 5
# Assembling Illumina + PacBio (CLR) reads
perl ${WG} -x pacraw -a M -s ecoli/reads/EC.50X.R1.fastq.gz,ecoli/reads/EC.50X.R2.fastq.gz -l ecoli/reads/EC.PAC.30X.fa.gz -p ec_Wm_pr1 -t 10 -g 5
Expected results
The fasta file *.SPolished.asm.wengan.fasta (ec_Wm_or1.SPolished.asm.wengan.fasta and ec_Wm_pr1.SPolished.asm.wengan.fasta respectively) contains the final genome assembly reported by Wengan. Both hybrid datasets are assembled to a single contig sequence (Genome Size of ~4.6 Mb).
Computational resources
The expected runtime with a single core is about 10 minutes and with 10 cores about 2 Minutes. The maximum RAM usage is around ~3 Gb.
Assembling human genomes
The supplementary material of the Wengan BioRxiv preprint describes the datasets and commands used to assemble four human genomes with Wengan.