-
I am running into a "Assertion `cnt > 0' failed" error in the assembly stage 4-unitigger. This is running on a cluster and so far this assembly ran without problems. I have restarted canu twice but th…
-
Hi,
I proceeded with pacbio assembly using canu 1.6.
The genome size of this sample is expected to be between 3.8 and 4.1 g, but the output of canu is about 4.6 g. (For reference, when we proceeded…
-
It takes one week to just generate 28 M 'fragment_file' and I don't know how long does it take.
Is there have parameters or ways to run this with multi-thread?
-
Hi @pb-jchin :+1:
Thanks for this nice assembler. I have a question on output primary contig and haplotigs. My fungus is highly heterogyzous, ~10 SNPs/kb. Here is some general summary of my assemb…
-
Hi, stschiff
When I prepare the input file for MSMC and run. it occurs Segmentation fault. Need I recompile on my computer ?
> read 1417 SNPs from file pre_input/preinput
> estimating scaled mutation…
-
I have successfully annotated my vcf file using a local installation of variant effect predictor (VEP). However, the filtering doesn't work. E.g. the command
`filter_vep -i vep.test.vcf.gz -filter …
matmu updated
5 years ago
-
Dear Koren, Walenz and Phillippy,
This is not an issue but rather query on canu bundling phasing ability for the diploid genome. I attended PAG2018 conference and had nice conversation with Koren …
-
I get this error on one partition when correcting reads from a about 60x coverage PacBio (P6C4 and Sequel) dataset for a fish.
`Processing read 5101649 of length 16844 with 531 evidence reads.
falco…
-
Hi,
@sjackman advised me to run ntCard on my raw data in https://github.com/bcgsc/abyss/issues/178#issuecomment-364214206 . Are you sure the output files can be parsed by GenomeScope http://qb.cshl…
-
re. biomarker_type
The biomarker_type list is legitimate as it comes directly from MM. They report a set of biomarker types per variant.
The lack of a cna seems to be purposeful.
# Note…