Tools to view fastq file

Question

[Roden Luo]

Hi,

I am curious about whether there is a tool for us to VIEW fastq file(NGS raw data). Like IGV, we can view sam/bam files to get some insights or check the results. So what I am looking for is a tool that can show the sequences and qualities of a small number of reads(e.g. less than 20). My idea is to use the brightness/depth of color to show the qualities. What's more, I hope I can drag the reads to align/compare them with each other in order to get some insight from doing so.

I have searched on google by keywords "(the best) tool to see/view fastq". But all the results are related to the processing of fastq files, NOT VIEWING.

So, is there a tool for that?

If not, anyone has the same need as I do? Is it worthy to develop one?

Many thanks,
Roden

[Michi]

Hi:

fastq files are normally just sequences without the information where in the genome they align - so IGV and other genome browsers cannot really reperesent it accurately

[Roden Luo]

Yeah, so what I am looking is a little bit like: IGV without reference, and I can even drag(e.g. horizontally or vertically) the reads to align manually.

Also like: I want to align/assemble about 20 reads in fastq format MANUALLY and see the results. Because I think if the amount of reads is not so huge, I can do it by my self and compare it to the results from other tools. But I do not want to do it by pen and paper.

[cpcantalapiedra]

umm not sure that a tool like that exists. Maybe because just running a classic assembler for Sanger sequences or maybe Velvet, spades or ssaha should be enough. Later you could align you sequences to the assembly and watch the alignments with IGV.

Answer 1

[openpaul]

If you really just want to have a quick glance at your data, have a look into fqless: https://github.com/openpaul/fqless

I wrote this small piece of software as I wanted to peak into sequencing reads without much hassle. It actually does color code the reads as you suggested, but you can not interact with anything. Just observe.

[John]

For the job it does, this is really great - nice one :)

Answer 2

[Benn]

You can use fastQC tool to see the quality of your reads.

If you want to look at the raw data, use a text editor or the bash command line

head file.fastq

or

cat file.fastq

[Roden Luo]

Thank you b.nota!

Sorry I did not make it clear. I knew that I could head or cat and see the plain-text style of the reads. But what I am looking is to VIEW vividly. Like IGV without reference, and I can even drag(e.g. horizontally or vertically) the reads to align manually.

[5heikki]

So something like:

head -n40 file.fq | fq2fa - | muscle -in - -out pointlessAlignment.fa

Answer 3

[Michael]

There are some GUI tools mostly for windows, like this one http://www.dnabaser.com/download/nextgen-fastq-editor/ which maybe allow for some individual interaction.

[Roden Luo]

I am going to try and give some feedbacks. Thank you Michael!

Answer 4

[Naren]

Geneious on trial version.

Answer 5

[nora]

try with wordpad to to observe the contents of fastq