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.

alephreish / fastqtiler