gapless

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Hello @schmeing I changed the Hi-C scaffolding algorithm (YAHS to EndHiC) and a previous issue with pure deletions went away, but now I got an issue with the duplication boolean...

grpiccoli

large genome changes

14

Thanks for a very interesting tool! I'm working with a very large (>20 Gb) draft genome assembly, so the default index size of 4 Gb for minimap2 requires 6 passes...

rwhetten

pipeline crashed : scaffold (Scaffold graph is inconsistent)

1

Hi, I only managed to run `gapless` on my ONT assembly (~400 contigs, haploid genome size of 3.1Gbp, there are no gaps in contigs) up to `gapless.py scaffold` stage in...

Duda5

pipeline crashed : scaffold (unexpected keyword argument 'nonpositive')

1

Hi, I have run the pipeline but i crashed in the first run. This is my script: ``` gapless.sh -j 32 -i genome.fa \ -t nanopore prome_filtered.fastq \ -n 3...

DiegoSafian

failed to run the gapless.sh

3

Hi, I downloaded the gapless-0.4 and ran the gapless.sh sh gapless.sh -j 40 -i genome.fasta -t nanopore porechop_output.fastq.gz -o /mnt/project/IPV2/gapless/gapless/final_output_assembly/ But it is showing the following error gapless.sh: line 162:...

kovimallik