Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
New feature: --cut-adapters (optional)
Description: Runs the FASTQC report on the raw sequence and generates a custom.fa adapter file using the FASTQC report on overrepresented sequences. Finally, passes the custom.fa adapter file to trimmomatic to cut the adapters and overrepresented sequences.
Usage: kneaddata -i seq.fastq -db demo_db -o kneaddata_output --cut-adapters --fastqc FastQC
Dependency: FastQC