https://github.com/asadprodhan/amr_detection_workflow
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: asadprodhan
- Default Branch: main
- Size: 1000 Bytes
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Antimicrobial Resistance Detection Workflow
M. Asaduzzaman Prodhan*
FastQC Analysis
Step 1: Bring the raw data in the Terminal
Open the Termnal
write cd and then drag the directory containg the fastq.gz files. It will show as follows:
cd "path-of-the-directory"
Hit enter
Check the fastq.gz files by running
ls
Step 2: Set a conda environment
Run the follwoing commands one by one
conda
If it shows the usage options, then you have conda installed. If it show "command not found", then you don't have conda installed. To install conda follow: https://github.com/asadprodhan/A-beginner-s-guide-to-Bioinformatics#how-to-install-conda-in-my-computer
Now, run
conda create -n amr
conda activate amr
conda install -c bioconda fastqc
Step 4: Create a directory to collect the fastqc results
- Create a directory to collect the fastqc results
mkdir fastqc_results
Step 5: Run FastQC
for file in *.fastq.gz; do fastqc $file -o ./fastqc_results/ -t 16 -Xmx20g; done
Then
cd fastqc_results
ls
You will see the fastqc reports here.
Owner
- Name: Asad Prodhan
- Login: asadprodhan
- Kind: user
- Location: Perth, Australia
- Company: Department of Primary Industries and Regional Development
- Website: www.linkedin.com/in/asadprodhan
- Twitter: Asad_Prodhan
- Repositories: 2
- Profile: https://github.com/asadprodhan
Laboratory Scientist at DPIRD. My work involves Oxford Nanopore Sequencing and Bioinformatics for pest and pathogen diagnosis.
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