eclarke / fqscan

Scans a directory of (optionally paired) FASTQ files for the prevalence of particular targets

fqscan

Scans a directory of (optionally paired) FASTQ files for the prevalence of particular targets

Installation

You will need bwa and samtools, or vsearch and seqtk installed to use.

git clone https://github.com/eclarke/fqscan
pip install fqscan

Usage

Let's assume you have directory full of demultiplexed FASTQ files in data_files and a FASTA file of sequences you want to scan the FASTQ files for in targets.fasta.

Using BWA

First build an bwa index for it using bwa index targets.fasta, then run:

fqscan targets.fasta data_files

Using vsearch

No indexing is required. Simply run:

fqscan --use_vsearch targets.fasta data_files

Paired samples

The default behavior is to consider each FASTQ separately. If you have read pairs, you can use the --pair option to consider the pair together when mapping. If you use vsearch, this will merge the reads before searching and discard any that don't pair.

Output

The program will output the number of reads that matched the target sequences in each file or read pair:

> fqscan targets.fasta data_files
sample1_R1.fastq sample1_R2.fastq 1245
sample2_R1.fastq sample2_R2.fastq 192