Human Viral Reconstruction Survey - Comparative evaluation of computational methods for reconstruction of human viral genomes
Run the whole experiment in a Linux system with:
git clone https://github.com/viromelab/HVRS.git cd HVRS/src/ bash Installation.sh --all bash Simulation.sh bash Reconstruction.sh --all bash Evaluation.sh bash Plots.sh
The survey includes the following tools:
| Tool | URL |
|---|---|
| coronaSPAdes | https://github.com/ablab/spades |
| Haploflow | https://github.com/hzi-bifo/Haploflow |
| IRMA | https://wonder.cdc.gov/amd/flu/irma/ |
| LAZYPIPE | https://www.helsinki.fi/en/projects/lazypipe |
| metaSPAdes | https://github.com/ablab/spades |
| metaviralSPAdes | https://github.com/ablab/spades |
| PEHaplo | https://github.com/chjiao/PEHaplo |
| QuRe | https://sourceforge.net/projects/qure |
| QVG | https://github.com/laczkol/QVG |
| SPAdes | https://github.com/ablab/spades |
| SSAKE | http://www.bcgsc.ca/bioinfo/software/ssake |
| TRACESPipe | https://github.com/viromelab/TRACESPipe |
| TRACESPipeLite | https://github.com/viromelab/TRACESPipeLite |
| VirGenA | https://github.com/gFedonin/VirGenA |
| ViSpA | https://alan.cs.gsu.edu/NGS/?q=content/vispa |
| V-pipe | https://github.com/cbg-ethz/V-pipe |
To see the possible installation options type
./Installation.sh -h
This will print the following options:
------------------------------------------------------------------
Installation.sh : Installation script for HVRS
Script to install all of the tools necesary to run HVRS.
Program options --------------------------------------------------
-h, --help Show this,
--miniconda Install Miniconda,
--all Install all tools, except Miniconda.
--coronaspades Install coronaSPAdes,
--haploflow Install Haploflow,
--irma Install IRMA,
--lazypipe Install LAZYPIPE,
--metaspades Install metaSPAdes,
--metaviralspades Install metaviralSPAdes,
--pehaplo Install PEHaplo,
--qure Install QuRe,
--qvg Install QVG,
--spades Install SPAdes,
--ssake Install SSAKE,
--tracespipe Install TRACESPipe,
--tracespipelite Install TRACESPipeLite,
--virgena Install VirGenA,
--vispa Install ViSpA,
--vpipe Install V-pipe,
--tools Install other tools used in the
benchmark.
Examples ---------------------------------------------------------
- Install Miniconda
./Installation.sh --miniconda
- Install all tools (except Miniconda)
./Installation.sh --all
------------------------------------------------------------------
To see the possible reconstruction options type
./Reconstruction.sh -h
This will print the following options:
------------------------------------------------------------------
Reconstruction.sh : Reconstruction script for HVRS
Script to reconstruct all of the datasets contained in HVRS.
Program options --------------------------------------------------
-h, --help Show this,
--all Reconstruction using all tools,
--coronaspades Reconstruction using coronaSPAdes,
--haploflow Reconstruction using Haploflow,
--lazypipe Reconstruction using LAZYPIPE,
--irma Reconstruction using IRMA,
--metaspades Reconstruction using metaSPAdes,
--metaviralspades Reconstruction using metaviralSPAdes,
--pehaplo Reconstruction using PEHaplo,
--qure Reconstruction using QuRe,
--qvg Reconstruction using QVG,
--spades Reconstruction using SPAdes,
--ssake Reconstruction using SSAKE,
--tracespipe Reconstruction using TRACESPipe,
--tracespipelite Reconstruction using TRACESPipeLite,
--virgena Reconstruction using VirGenA,
--vispa Reconstruction using ViSpA,
--vpipe Reconstruction using V-pipe.
-t <INT>, --threads <INT> Number of threads,
-m <INT>, --memory <INT> Maximum of RAM available,
--virgena-timeout <INT> Maximum time used by VirGenA
to reconstruct with each reference,
--timeout <INT> Maximum time used by a reconstruction
program to reconstruct a genome.
-r <STR>, --reads <STR> FASTQ reads file name. The string
must be the name before _1 and _2.fq.
The references are retrieved using
FALCON-meta.
-y, --yes Assume the answer to all prompts is yes.
--top_falcon <INT> Maximum number of references retrived
by FALCON-meta.
Examples ---------------------------------------------------------
- Reconstruct using all tools
./Reconstruction.sh --all
------------------------------------------------------------------
On using this software/method please cite:
- pending
For any issue let us know at issues link.
GPL v3.
For more information:
http://www.gnu.org/licenses/gpl-3.0.html