Hello,

I have downloaded SRA data from NCBI and converted it into Fastq file (Pair end sequences), then I analysed the sequences using fastqc. The following results I got, which I think ok. But still confuse. Can anybody shade some light on this aspect. (Per base sequence quality http://dropcanvas.com/#aG53s1AtEBgLv1)

##FastQC    0.11.2
>>Basic Statistics  pass
#Measure    Value
Filename    PPlf.fastq
File type   Conventional base calls
Encoding    Sanger / Illumina 1.9
Total Sequences 24000000
Sequences flagged as poor quality   0
Sequence length 75
%GC 44

Can I use fastq sequences derived from SRA format directly for assembly and scaffolding purpose? Or else I will have to do pre processing like removal of low quality reads,trimming of low quality bases,adapter removal?

regards
rahul