How to convert fastq file with raw reads to draft genome fastq file ?

Question

[gskbioinfo143]

Hi sir/mam,

i have done mapping of Streptococcus pneumonia raw sequenced data with reference Streptococcus pneumonia ATCC 700669 using bowtie2. i have converted from .bam file to .fasta file. the fasta file it has the raw reads - that is the fasta file just stripped of the quality scores know how to get draft genome fasta file.

fasta read image https://ibb.co/cMDzRQ

Need help

thanks

[Brian Bushnell]

It sounds like you are trying to assemble a library. In that case, I'd suggest preprocessing the data to clean it up, then assembling it with Spades to yield a draft genome. Mapping to a related genome is not usually part of this process unless you are trying to reduce contamination or you want to do a reference-guided assembly.

[gskbioinfo143]

Yes sir, im actually looking for reference based mapping of reads

[Michael]

not sure what you mean by "how to get draft genome fasta file", please explain better.

[Buffo]

You have to make an assembly "assembling", not mapping, if your reference is a very conserved specie you can make a guided assembly using spades, idba-hybrid or trinity, if it doesn´t, you have to make a "denovo" assembly in which case I would recommend you spades.

[gskbioinfo143]

http://spades.bioinf.spbau.ru/release3.10.1/manual.html

we cant do reference based mapping (assembly) with spades as given in spades manuel

thanks need your suggestions