fastqc

FastQC

About: |

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

Documentation : https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Citation : TBA

Directory tree:

fastqc
├── fastqc_summary.csv
├── sample_1_fastqc.html
├── sample_1_fastqc.zip
├── sample_2_fastqc.html
├── sample_2_fastqc.zip
└── sample_summary.csv

Example file for an individual sample (sample_summary.csv)

sample,FastQC,Basic Statistics,Measure,Filename,File type,Encoding,Total Sequences,Total Bases,Sequences flagged as poor quality,Sequence length
SRR7889058,0.12.1,pass,Value,SRR7889058_1.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,575024,117.3 Mbp,0,35-251
SRR7889058,0.12.1,pass,Value,SRR7889058_2.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,575024,117.9 Mbp,0,35-251

Example file for a run (fastqc_summary.csv)

sample,FastQC,Basic Statistics,Measure,Filename,File type,Encoding,Total Sequences,Total Bases,Sequences flagged as poor quality,Sequence length
82300018-UT-M70330-230725,0.12.1,pass,Value,82300018-UT-M70330-230725_S8_L001_R1_001.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,672047,159.7 Mbp,0,35-251
82300018-UT-M70330-230725,0.12.1,pass,Value,82300018-UT-M70330-230725_S8_L001_R2_001.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,672047,159.7 Mbp,0,35-251
SRR11725329,0.12.1,pass,Value,SRR11725329_1.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,544641,130.4 Mbp,0,35-251
SRR11725329,0.12.1,pass,Value,SRR11725329_2.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,544641,130.5 Mbp,0,35-251
SRR13643280,0.12.1,pass,Value,SRR13643280_1.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,528309,127.7 Mbp,0,35-251
SRR13643280,0.12.1,pass,Value,SRR13643280_2.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,528309,127.7 Mbp,0,35-251
SRR14436834,0.12.1,pass,Value,SRR14436834_1.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,414834,91.8 Mbp,0,35-251
SRR14436834,0.12.1,pass,Value,SRR14436834_2.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,414834,89.4 Mbp,0,35-251
SRR14634837,0.12.1,pass,Value,SRR14634837_1.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,594127,142.7 Mbp,0,35-251
SRR14634837,0.12.1,pass,Value,SRR14634837_2.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,594127,142.8 Mbp,0,35-251
SRR7738178,0.12.1,pass,Value,SRR7738178_1.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,500129,120.9 Mbp,0,35-251
SRR7738178,0.12.1,pass,Value,SRR7738178_2.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,500129,121 Mbp,0,35-251
SRR7889058,0.12.1,pass,Value,SRR7889058_1.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,575024,117.3 Mbp,0,35-251
SRR7889058,0.12.1,pass,Value,SRR7889058_2.fastq.gz,Conventional base calls,Sanger / Illumina 1.9,575024,117.9 Mbp,0,35-251