Oliver is right - find some bioinformatician and discuss your project with him, because:

1) If you have real NGS data you will have most probable millions (of millions) of reads. There is neither any good reason to manually inspect or edit such huge data files nor there is a special tool which allows you to do so in any fancy way. FASTQ is simple text, if you want to take a look into that file use any text editor - but again, i don't see the point in doing so.

2) Anything else depends on the type of your data and the project. As already mentioned, processing of FASTQ data can involve many consecutive steps from simple processing and quality filtering to mapping, alignment, assembly, gene finding, and may many more. Without any information about what you're trying to answer using your NGS data it's impossible to give you any help. Even though you know in the end what to do you will most probable need someone experienced in order to carry out your bioinformatic analysis. I worry that this is beyond the capabilities of the question system here on research gate.

fastq files are simple text files you don't need any special software to view them other then a text editor like notepad,wordpad or vi (in case of Linux/unix).

Thanks but probably i didn't know how to put the question across. How can i view the files then? How can i view, edit and create

alignments with the sequences?

You need fastqc for view and for editing u will need other tools for filtering and trimming and then you can use these file for alignment.

As Inder Rawal said fastq is a particular text fromat. So you can open them and view your reads with any text editor.

Fastqc is for checking the quality of your data: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

If you want to map ( your reads against a reference), align, ("edit" to use your words) you have tools as BWA(http://bio-bwa.sourceforge.net/), samtools(http://samtools.sourceforge.net/).

Yeah u ll need other softwares to align and edit ur fastq reads as suggested by vishal and Ayite. The general flow of work would b sumthng like this:

1: preprocess the files (sequence reads)- this will include removing adaptor sequence in the reads and it's necessary to remove those sequences before u map (align) it to any reference genome/transcriptome. And may b low scoring ends of the reads. For initial preprocessing u can use tools like fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)

2: Quality checks- u can use fastqc as suggested above to see the quality of reads.

3: Mapping/ aligning ur reads (fastq files) to a reference genome/transcriptome. Here also many options are available u can use BWA, Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) and there many other same softwares. My personal experience wid bowtie has been gud so I Wud recommend that.

4: Analyis: once u map/align ur reads u ll hv .sam files or .map files as d output, d latter being d old format. .sam files ll hv all d information about d mapping like where ur read is mapping in d reference genome n if it's in exonic region etc. From here u can convert ur files to bam files using samtools and do analyses based on ur needs.

This is d very generalised outline u might hv to change n try few more things according to ur needs. N to do all this at a single place u can use galaxy server (https://usegalaxy.org/). The only limitation here is d size of files it can handle but if ur files r within its size limits then it's very easy to use tool. In d end one thng I Wud suggest is before u get started read abt the file formats then u ll b able work wid less issues.

GALAXY is a great resource that contains all of the programs you will need. The only problem I have with it is transferring files to the Penn server, but you can also run a local install.

Would have been better to think about this before spending a lot of money :)

Would be best to ask someone, bioinformatician, for help. Otherwise it will take you months... or years... but Galaxy is probably the best option if you don't have local access to a server. What kind of experiment is it, RNA-seq ?

Oliver is right - find some bioinformatician and discuss your project with him, because:

1) If you have real NGS data you will have most probable millions (of millions) of reads. There is neither any good reason to manually inspect or edit such huge data files nor there is a special tool which allows you to do so in any fancy way. FASTQ is simple text, if you want to take a look into that file use any text editor - but again, i don't see the point in doing so.

2) Anything else depends on the type of your data and the project. As already mentioned, processing of FASTQ data can involve many consecutive steps from simple processing and quality filtering to mapping, alignment, assembly, gene finding, and may many more. Without any information about what you're trying to answer using your NGS data it's impossible to give you any help. Even though you know in the end what to do you will most probable need someone experienced in order to carry out your bioinformatic analysis. I worry that this is beyond the capabilities of the question system here on research gate.

Completely agree with both Sebastian and Oliver.

Depends on what you want to do. Many free tools online. If you just want to "open" it, use notepad.