fqTooling

A command line FASTQ file toolbox

primerFind

Find and summarize the presence of given primers (or any subseq) within a fastq file

Usage

python3 primerFind.py -s <sequenceFile> -p <primerFile>

-v/--verbose - gives debug output -r/--reporting - creates report files based on hits found

FastQC Pipeline

A straightforward program which can take a file list of fastq's, concatenate them, and perform FastQC on them in serial or scalable parallel

Requirements

Python - built on 3.10x but should be fine for the forseeable future
FastQC - the underlying tool to perform QC on your read files
Bash Environment - current mechanics rely on system calls to the bash command line

Input File

File structure should follow the convention SampleID_Lane#_Read#.fastq. For example: Exp001_S1_L002_R1_001.fastq

FastQC Pipe expects a tab-delimited text file with the following structure (lines led with '#' are ignored):

Path/of/directory | Sample_Name | R1/2/Both

Example:

/home/RPINerd/M01234/Fastq_Generation Exp001_S1   2
/home/RPINerd/M01234/Fastq_Generation Exp001_S2   1
/home/RPINerd/M01234/Fastq_Generation Exp001_S3   Both

Running Pipeline

General format for run is python3 fastqc_pipe.py -f file_list.tsv

The input file is the only required argument however there are some additional options:
--threads or -t # specifies how many threads to allocate to the fastqc algorithm, currently capped at 12
--merge or -m <desired/path/to/> allows for a preferred location to be specified for the merged lanes to be written to
--verbose or -v pumps out a ton of extra info and saves it to the file fastqc_pipe.log

fastq_filtering

Provided a single, or list of, regular expressions, filter out all reads from a given fastq file which match said expression(s).

One use case could be dropping reads with a large amount of poly-A sequences:

python fqfilter.py -f Sample01.fastq -d "[A]{25}"

Or perhaps you have a specific adapter at the start of the read that you'd like to isolate

python fqfilter.py -f Sample01.fastq -k "^ATCGGCTA"

And you can also do both at once!

python fqfilter.py -f Sample01.fastq -k "^ATCGGCTA" -d "[A]{25}"

Options

-f/--fastq	Input fastq file to filter
-p/--pair	Input pair of fastqs. R1 then R2. Files will be syncronized in the ouput for safety of downstream processing!
-k/--keep	Regex expression(s) to keep
-d/--drop	Regex expression(s) to drop
-s/--sync	Synchronize R1/R2 fastq's for downstream processing
-v/--verbose	Debug output

Requirements

Built on Python 3.11, but may be fine back as far as 3.7
Needs the BioPython package