I have sequenced my Bacteria using NGS and got fastq data. For analysis now I need to convert this data into FASTA. How can I do that easily? Should I use galaxy or recommend any other good tool?
Thanks in advance.
There are hundreds of way to do that and tens of online tool available. But this is not you should do to proceed.
Also, highly recommend is to learn the basics of analysis before proceeding further with your analysis.
Is your fastq file single file (single reads) or two files with F.fastq and R.fastq (end-paired reads). Is this file generated after sequencing ( short or long reads?). Normally, if this file is single or end-paired reads generated from NGS, you must go for fastQC or FastQ info analysis to check the quality of reads, adapter and primer contains in the read sequence. You can trim those adapters or primer if present using many tools like trimmomatic (Illumina NGS) or fastq.... later you should perform assemble... after that you will get fasta file...
The above-mentioned is meant for whole-genome sequencing. For 16S amplicon metagenome, transcriptome,... etc sequencing read file, you have to perform in different ways....
@Roman Naorem, my fastq paired-end files, short read, yes after whole genome sequencing.
If you are not Linux friendly and no knowledge of coding/ script. Then create user name and password in galaxy Europe server by registration. After that import your files in it. Follow the steps: check for fastQC and trim the adapters and primer if present using trimmomatic for both reads, in that use the option of trim based on your sequencing platform. After that check once more the presence of adapters. If the quality is good then you can proceed for assembly using spades, or velvet, after that you will get the fasta contigs
DEAR Shahina Akter
(see http://maq.sourceforge.net/fastq.shtml )
GOOD LUCK
Easiest way is to use seqtk - a python module.
If you don't have it just use pip3 to install it.
pip3 install seqtk
Then do as follows:
seqtk seq -A fastq-file
That should do it.
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