byronmews / qc-trim-screen Goto Github PK

Run as either PE or SE versions.

Requires: qc_results_parser_[se|pe].pl from repository

Uses fastqc, trimmomatic, fasqtc_screen and summarises results into single table.

If running PE version all PE fastq within folder are analysed, using the string before illumina sample index number as sample ID.

$ bpipe run -r qc_trim_screen_pe.groovy *

Produces the following files with suffixes or names:

• fastqc_pre_qc/.html: fastqc output before trimming
• PE.fastq|SE.fastq: four trimmed fastq output files, both PE and orphan SE
• fastqc_pre_qc/.html: fastqc ouput after trimming
• PE_no_hits_file.1.fastq/PE_no_hits_file.2.fastq: Human host and UniVec unmapped reads for each pair
• PE_screen.png: Human host and UniVec unmapped read distribution
• qc_summary_stats.tsv: qc summary metrics

Also requires:

• FastQC
• Trimmomatic
• Bowtie2
• Fastq_screen (http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)

Fastq screen uses bowtie2 indexes of human assembly GRCh38 and the Univec v8 database (ftp://ftp.ncbi.nlm.nih.gov/pub/UniVec/)