alephreish / fastqtiler

Read quality visualization for Illumina sequencing runs

fastqtiler

This is a program for read quality visualization of Illumina sequencing runs.

Installation

• Clone the repository:

    git clone https://github.com/har-wradim/fastqtiler.git
  

or download the files as zip

• Optionally copy the scripts somewhere to your PATH:

    sudo cp fastqtiler/*.pl /usr/local/bin
  

• For the fastqtiler program to work ensure that ImageMagick is installed and convert is available in the PATH.

Launching the program

Depending on how you installed the program you can either launch it as fastqtiler.pl, ./fastqtiler.pl or perl fastqtiler.pl.

The general form of the command looks like fastqtiler.pl [parameters] [files]

Parameters

Short	Long	Description	Default value
-k	--kit	sequencing kit/flowcell type (see below)	none
-n	--name	name for output files	tiles
-o	--outdir	output directory	.
-t	--threads	max number of threads	2
-l	--len	read length	taken from the first read
-f	--frac	fraction of the reads to analyze	0.01
-s	--scale	scale factor (pixel size in FC units)	1000
-g	--goodcolor	color for the high-quality bases	magenta
-b	--badcolor	color for the low-quality bases	green
-i	--lanemin	lane number reads start at	1
-j	--lanemax	lane number reads end at	kit-specific
-h	--help	output the help page
-v	--version	same as above

The --kit options is mandatory. The supported kits are as follows:

Kit	Full value	Alternative shortcuts
HiSeq 2000 or 2500, High Output	hiseq2000/2500:high-output	hiseq2000:high-output, hiseq2500:high-output, hs2000:ho, hs2500:ho
HiSeq 2000 or 2500, Rapid Run	hiseq2000/2500:rapid-run	hiseq2000:rapid-run, hiseq2500:rapid-run, hs2000:rr, hs2500:rr
HiSeq 3000 or 4000	hiseq3000/4000	hiseq3000, hiseq4000, hs3000, hs4000
HiSeq X	hiseqX	hsX
MiSeq	miseq	ms
MiSeq Micro	miseq:micro	ms:micro
MiSeq Nano	miseq:nano	ms:nano
NextSeq 500 or 550, High Output	nextseq500/550:high-output	nextseq500:high-output, nextseq550:high-output, ns500:ho, ns550:ho
NextSeq 500 or 550, Mid Output	nextseq500/550:mid-output	nextseq500:mid-output, nextseq550:mid-output, ns500:mo, ns550:mo

If you don't know the kit used you can always run the fastqtester.pl script providing it your file(s) (one exemplary file would suffice). It will also output some other useful information

Input files

Either gzipped, bzipped or raw fastq, but not a mix of different types.

Output files

As output you will get a folder with the images corresponding to the quality scores at each one of the sequencing cycles and an html report. Here is how a good run looks like and here is a bad one.