fastq to full genome

Question

[Eva_Maria]

Hai

I want to convert fastq (both forward and backward) of a bacterium and corresponding reference sequence . I want to convert that into full genome. which tool is useful to do this?

[Michael]

Hi, you might not get the desired answer because your question is ambiguous, please explain which data you have. If you have fastq reads and a reference sequence, what is the difference of your reference to a 'full genome'? Do you want to assemble the reads?

[Eva_Maria]

i want to assemble my reads into full length.

Answer 1

[kapil.joshi036]

actually u can easily convert fastq file to fasta with generation of qual file

awk 'BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}' input.fastq > output.fasta

[Naren]

may be he wants to assemble reads to genome (contigs/ scaffolds) based on ref. genome

[Eva_Maria]

yes i want to assemble reads