bbduk

BBduk

About: |

filters or trims reads for adapters and contaminants using k-mers

Used for phix removal in fastq files.

Documentation : https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/

Citation : https://jgi.doe.gov/data-and-tools/software-tools/bbtools/

Directory tree:

bbduk
├── sample.matched_phix.fq
├── sample.phix.stats.txt
├── sample_rmphix_R1.fastq.gz
├── sample_rmphix_R2.fastq.gz
├── sample.matched_phix.fq
├── sample.phix.stats.txt
├── sample_rmphix_R1.fastq.gz
└── sample_rmphix_R2.fastq.gz

Example file for an individual sample (sample.phix.stats.txt)

#File	82300018-UT-M70330-230725_S8_L001_R1_001.fastq.gz	82300018-UT-M70330-230725_S8_L001_R2_001.fastq.gz
#Total	1344094
#Matched	8	0.00060%
#Name	Reads	ReadsPct
gi|9626372|ref|NC_001422.1| Coliphage phiX174, complete genome	8	0.00060%

no per run file