Entering edit mode
6.1 years ago
gskbioinfo143 ▴ 60
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
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.
Yes sir, im actually looking for reference based mapping of reads
not sure what you mean by "how to get draft genome fasta file", please explain better.
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.
we cant do reference based mapping (assembly) with spades as given in spades manuel
thanks need your suggestions