ChakrabortyLab

icon indicating a website link https://chakrabortylab.org/

icon company Texas A&M University icon location College Station icon location Trying to understand the cause and consequences of genetic variation.

Results 69 comments of ChakrabortyLab

Is there a way to run quickmerge wrapper in multi-threads?

You can use mummer 4 which uses multi threading. You can run quickmerge manually after that. On Thu, Nov 21, 2019, 18:15 ShuChen1986 wrote: > Hi, > > I am...

Is there a way to run quickmerge wrapper in multi-threads?

sorry for the late response. MUMmer v4 supports multi-threading for both sam and delta. run nucmer like this - nucmer --threads 4 --prefix foo ref.fasta query.fasta [assuming that you are...

hybrid assembly

It can't. You can dbg2olc. On Thu, Oct 17, 2019, 18:44 Michał T. Lorenc wrote: > Hi, > We have 50x Illumina paired-end and 7x ONT reads. Is QuickMerge able...

Is there a history of merges not included in anchor_summary.txt?

This could potentially be a bug. I'll need to check what happened. Will you be able to share your files (fasta & delta) ? On Tue, Jun 22, 2021, 01:47...

Quickmerge before or after haplotype purging for high heter rate plant assemblies?

Hi Kun, It is better to remove the redundant sequences, although probably not necessary. Perhaps try it without removing them and see what happens. But removal of the redundant sequences...

terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 1047464) > this->size() (which is 0) Aborted

do the sequence names have white space in them? On Fri, Oct 22, 2021 at 5:24 AM yangxiaofeill ***@***.***> wrote: > I also have this problem. > > terminate called...

confused about the results: sv.txt and cnv.txt

The SV.xx.txt file has a comprehensive list of SVs, but some CNVs, especially in highly repetitive sequences can be missed and not present in this file. It's probably okay to...

confused about the results: sv.txt and cnv.txt

To the best of my knowledge, they're 1-based. On Sun, Jan 8, 2023 at 2:26 AM Hui ***@***.***> wrote: > Hi! > I'm sorry to bother you, but I have...

lastz or Mummer

Hi, SVMU gives preference to MUMmer because I am yet to figure out the best way to resolve incongruence between the two aligners. On Sun, Jul 26, 2020 at 6:45...

Quickmerge fails to set its PATH internally

@jgbaldwinbrown @esolares can we fix this?