Have you already tried readseq? Otherwise, if you can handle the (Linux/Mac) unix commandline, you could use the attached simple python script (it requires python 2.7+ and biopython). Also the assembler IDBA comes with it's own fastq2fasta script (also unix based).

Why exactly do you want to convert it to Fasta? Fastq is currently the most common file-format for unassembled sequence reads and you'll loose all base quality information when converting it to fasta. Depending on what you are planning to do, you may not have to convert it.

Dear John Vollmers I have not tried for readseq and also am not using Linux/Mac. I want my raw data file in FASTA format as am unable to open FASTQ file in windows 8.1.

Recommend a solfware: " UltraEdit ", it can open FASTQ file in windows , but if you want to convert FASTQ to FASTA format, there are lots of solfware you can adopt, like the script " fastq2fasta.py" offered by John Vollmers , others like "Fastx-tookit" also can solve this problem! but all of them work in Linux/Mac ! Maybe you can use the solfware " CLC Genomics Workbench", it can work in windows, but it will need large hardware, such as memory! best wishes to you

Dear Ma Wuqiang thank you so much.

Dear sharma,

Kindly tell me what you want to do and the software you are using

Hi Jyoti Sharma,

Have you converted FastaQ into FASTA sequnce?

Even when this is an old question, but I just ran into it and thought to leave for future references the 'common' solution for Linux/bash:

sed -n '1~4s/^@/>/p;2~4p' in.fastq > out.fasta

Well this might help anyone who comes across your question of how to converted fastq files to fasta, bellow is a simple way to do that.

1. You have to install a package called seqtk using bioconda for Linux users(biolinux or obuntu)

2. On your terminal $ seqtk seq -A input_file.fastq > output_file.fasta

You good to go!

seqtk seq -a file.fq > file.fna

https://github.com/lh3/seqtk

perl command to convert fastq file into fasta file

perl -ne 'y/@/>/;print($_.)&&&&' your_file.fastq > output_file.fasta

a late addition, but perhaps useful to some:

usegalaxy.org has several converters. Accounts are free, and it's not too difficult to get started.

Check this https://reneshbedre.github.io/blog/format.html

try here website

Try seqtk:

https://github.com/lh3/seqtk

with the command

seqtk seq -a in.fastq.gz > out.fasta

This is awfuly late but for anyone looking for another answer, I have used Galaxy (test.galaxyproject.org) and used the FASTQ to FASTA converter. However, it will depend whether your file is a single-read run or a paired-end run to generate a single file. But I recommend you to trim your sequence before using the converter to eliminate adapter sequences.

Awk and shell sometimes do not work for multi-line records.

Seqtk, BioPerl or BioPython may be a better alternative.

Use the Galaxy project (https://test.galaxyproject.org/).

You will have to upload your sequence and then type "FASTQ to FASTA converter" in the search engine. It will take a bit but you can copy the output.

https://usegalaxy.org/

Covert Formats --> FASTQ to FASTA converter

use bioawk

READS=[your reads basename]

bioawk \

-c fastx \

'{ print ">" $name "\n" $seq }' \

$READS.fastq \

> $READS.fasta

Very useful set of tools was developed by Wei Shen

https://github.com/shenwei356/seqkit

In your case this command should work:

seqkit fq2fa input.fq -o output.fasta

Dear Jyoti Sharma

Check this link if you are fan of command line :)

https://bioinformaticsworkbook.org/dataWrangling/fastaq-manipulations/converting-fastq-format-to-fasta.html#gsc.tab=0

u may use galaxy platform there is a convertor