SRA reads from NCBI + Nanopore

alekseyzimin / masurca

GNU General Public License v3.0

237 stars 35 forks source link

SRA reads from NCBI + Nanopore #98

Open madhubioinfo opened 5 years ago

madhubioinfo commented 5 years ago

Hi, I am trying to use Nanopore and some illumina reads from SRA database, I provided the fastq file from SRA its not working with the file, is there any way that can i use the fastq downloaded file for asembly

my Reads looks like this @SRR2727626.1.1 HWI-D00104:220:C42R8ACXX:2:1101:1345:2204 length=50 GTAATTCCAAATCTCGATCTATGAATTTTTAAAAAGTAATCTCAAACCTC +SRR2727626.1.1 HWI-D00104:220:C42R8ACXX:2:1101:1345:2204 length=50 9FFBFFBEF?3??8*CEGFCD9FF@@CGIIHFA,BDHF=FDDDBB@;?

Thank you

alekseyzimin commented 5 years ago

This is perfectly fine fastq file, but the reads are only 50bp long. The assembly will be very poor.

madhubioinfo commented 5 years ago

I tried avoiding the MP data , with only PE and nanopore it generated only 80 Mb of assembly