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cschin / Peregrine

Peregrine: Fast Genome Assembler Using SHIMMER Index
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shmr_map issue #15

Open smoretti opened 4 years ago

smoretti commented 4 years ago

I have the same issue as the one mentioned in #10 Do you know what could cause this?

cschin commented 4 years ago

@smoretti do you have some background of the input data of your assembly run? CCS read, coverage? It looks that you don't get a draft assembly from the earlier step to me.

ghost commented 4 years ago

@cschin The input data was generated using two SMRT cells v3. The mean coverage over the two SMRT cells was ~ 68x. The two .subreads.bam files were used as input to create a single fasta file using Pacbio's bam2fastx.

cschin commented 4 years ago

@taneKFL it seems to me your data is PacBio's subreads rather than CCS reads. Currently, Peregrine is designed for accurate reads (>99% accuracy > 10kb length). The subreads won't have the accuracy for Peregrine to assemble.

ghost commented 4 years ago

@cschin okay - so I'll try running pbccs on both my movies, convert them to a single fastq using bam2fastx, then retry running peregrine.