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simoncchu / GAPPadder

GAPPadder is tool for closing gaps on draft genomes with short sequencing data
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Long and short reads for Gap filling #5

Closed alslonik closed 6 years ago

alslonik commented 6 years ago

Hi,

I am sorry if the question that I am asking has been in the paper, and I just missed the point but:

I have two types of reads and I want to to fill the gaps in Chromium 10x assembly -

  1. Illumina PE reads
  2. PacBio reads. Gappadder needs the alignments of the reads to be done before it fills the gaps. Therefore I am going to run bwa/bowtie on the Illumina reads (10x assembler does not output bam alignment files). What about the long reads? Can I use them to fill the gaps too?

Thanks

simoncchu commented 6 years ago

Hi, GAPPadder is designed for short reads only. So it cannot be used to fill the gap with long reads at the current stage.