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?
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
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.
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.
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.
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.
Obviously a very late response, here, but for anyone looking for answers now or in future:
I'm sure there are other tools, but the one I used as far back as ~ 2012-2013 was FinchTV, where you could/can visualize perhaps why some base calls were made. If I remember right, you insert/paste/upload a fastq file, and you can see the traces which I infer are (posterior?) distributions based on at least Phred scores (i.e. high scores have a narrow distribution/low uncertainty in the call; low scores have a wide distribution/high uncertainty in the call). How you can get non-normal shapes in some calls is curious, so there must be some information shared between calls, and again, probably not just Phred scores.
Anyway, hope this helps others out there. And if anyone knows of other software or R/Python packages that serve a similar function, please share!
FinchTV is meant for use with ABI chromatogram (sanger sequencing) files. Don't think it can read fastq files. In any case there is no call distribution available in fastq files since there is only a single basecall at each position and only one quality score associated with each base. Since there can be millions of fastq reads in every data file there is no point in trying to view individual fastq reads, like one does with FinchTV..
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
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.
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.