denv-reference-based-assembly
Science Score: 44.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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○Scientific vocabulary similarity
Low similarity (9.3%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: majkabio
- Language: Shell
- Default Branch: main
- Size: 70.3 KB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
DENV reference-based assembly
This script is a custom pipeline to perform referenced-based assembly of trimmed / filtered FASTQ files
by M Galarion
IMPORTANT DEPENDENCIES!!!
Make sure the following tools are installed:
minimap2 https://github.com/lh3/minimap2
samtools https://www.htslib.org/
bcftools https://samtools.github.io/bcftools/
medaka https://github.com/nanoporetech/medaka
Once these tools are installed, you need to explicitly define the command usage for each tool
To do this, open the latest version of the bash script in a text editor
Starting from around line 29, edit the line that corresponds to the tool definition (inside the quotation marks)
For example:
```
Define tools and how you call them in your current system
minimap2 = "minimap2" samtools = "samtools" bcftools = "bcftools" medaka = ". /home/user/medaka/venv/bin/activate" # activate medaka conda environment
```
The tool definition inside the quotation marks should correspond to how you call them in your current system
Save the bash file and close
The script is an executable file written in bash and performs the following steps:
- Aligns the reads to a reference file using minimap2
- Generates VCF file using bcftools mpileup
- Produces a draft consensus file using bcftools consensus
- Extracts mapped reads only using samtools and aligns them back to the draft consensus using medaka_consensus
- Medaka generates a polished consensus
- Masks low depth positions in the polished consensus using a user-specified minimum threshold
- Produces final alignment stats
Command line usage:
```
bash ref-based-assembly_v2.2.sh -i reads.fastq -r reference.fasta
``` NOTE: Always run the script inside the directory where your -i and -r files are located.
To print options and default values:
```
bash ref-based-assembly_v2.2.sh
Optional parameters:
-t: number of threads (default: 8)
-M: Medaka polishing model (default: r941minhac_g507m)
-m: minimum read length (default: 200)
-x: maximum read length (default: none)
-d: minimum read depth (default: 20)
-q: minimum read Q-score (default: 9)
```
Owner
- Name: Majo Galarion
- Login: majkabio
- Kind: user
- Repositories: 1
- Profile: https://github.com/majkabio
Citation (citation.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Galarion
given-names: Ma Jowina
orcid: https://orcid.org/0000-0003-0088-2093
title: "DENV reference-based assembly"
version: 2.2
date-released: 2024-07-07