Fastqc

FastQC is a program designed to spot potential problems in high througput sequencing datasets. It runs a set of analyses on one or more raw sequence files in fastq or bam format and produces a report which summarises the results.

Workflow

1. Input paired-end reads
   Upload R1 and R2 FASTQ files.

2. Run FastQC quality assessment
   Analyze both read files and generate standard FastQC reports.

3. Extract QC metrics
   Collect total sequence number, sequence length, GC content, and PASS/WARN/FAIL counts.

4. Generate reports
   Output an overall summary table together with FastQC HTML and ZIP report files for each read.

Data

Example dataset include 100 bp illumina WGS reads consist of ~10% subsets of 3 paired end sets of reads from the following publication:
The sample names in the original publication used to generate the toy dataset is ERR260162 (sample1)

Result

v0.1: The pipeline is stored in Code Repository: CRS1240379505139527680. The computational docker enrionment is stored in Software Repository: SRS1240804675067064320.

Reproducibility

The pipeline utilizes code CRS1240379505139527680 and Docker image SRS1240804675067064320, both of which are stored in the BMAP repositories.

Usage

1. Select the application 'fastQC'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters

5. Upload the compressed data in gz or rar format.