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Hi Warren,
I'm using LINKS v1.8.5 to scaffold the contigs produced by [MEGAHIT](https://github.com/voutcn/megahit).
I used hybrid reads including PE, MPE, and PacBio long-reads. The PE and MPE rea…
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I met this problem with error ' Waiting at most 10 seconds for missing files.
Error in job initialize_checkm while creating output files....
The checkm-genome version is checkm-genome: 1.0.7-py35_0…
ghost updated
6 years ago
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I am using canu 1.7 for assembling a genome of ~1.4gb size with ~70X pacbio data.
canu -p canu -d canu-pacbio useGrid=false maxThreads=60 maxMemory=500 genomeSize=1.4g -pacbio-raw file1 ....
I hav…
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The simplest idea is to take kmers (k = 5, 7, 10?) centered at variant positions and fit a distribution (beta distribution?) of artifact allele fractions for each kmer.
Back of the envelope: with…
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Peregrine fails to start with the kids first dictionary at https://s3.amazonaws.com/dictionary-artifacts/kf-dictionary/kf-v0.1.2/schema.json
Peregrine bombs out attempting to assemble '_related_cas…
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Hi,
for the last 3-4 weeks I am struggling with attemps to get the fish genome assembly (see issue #187). I received successfully k64, k96, k112, k128 assemblies but although I recompiled abyss wit…
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I've run canu-1.5 for a huge genome with (only) 25x PacBio data on a grid:
`./canu-1.5/Linux-amd64/bin/canu -correct genomeSize=huge(>10g) corErrorRate=0.02 batThreads=64 batMemory=250 maxThreads=1…
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```
bcalm -in pe400.in -out hsapiens-unitigs -k 64 -abundance 5 -nb-cores 32
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Kmer-counting wallclock: 45118.6 secs
post-kmer counting -- memory [current, maximum (maxRSS)]: [2044, 4573] MB
DSK u…
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Dear Authors hi,
As an ignorant visiting scholar about denovo assembly generation, I couldnt find detailed information in the canu wiki about, simply if my run was successfully ended or I need to t…
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