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Dear community,
The -c parameter is used to generate the consensus sequence,but it is too slow.
Can I use prefix.dmo.lay.utg as the final contig.fasta ?
Thank you.
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I am trying to run Masurca 3.2.8 on our new SLURM based cluster. I am assembling 40 Gb of Nanopore reads plus Illumina PE and Jump libraries. Masurca ran for a few hours and completed the read corre…
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Hello, I'm trying to run annotate_hits_pyseer using my unitig based hits. I can see my gff3 files have the following feature types so I'm not sure why the below command isn't working. I'm using Pyseer…
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There's a contig page for accessing the data, but there isn't a description of how the data was created and/or what meta-data is in the header of each fasta file. A description of this will ensure peo…
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Hi
I was doing genome assembly and
it seems that miniasm gives empty gfa file in step 3.
[M::main] ===> Step 1: reading read mappings Step 2: 1-pass (crude) read selection Step 3: 2-pass (fin…
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* OS: OS X
* Command: `bcalm -in "hg38/hg38.fna" -out "hg38/hg38.bc31.fa" -kmer-size "31" -nb-cores "1" -abundance-min 1`
* Dataset: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz…
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there are reasons why this kind of thing wouldn't always work, but even that could be interesting.
we could use Luiz's MAG search (https://blog.luizirber.org/2020/07/24/mag-results/) to see if puta…
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I've run fermi on a very small dataset containing 22 fasta records using the following cmd:
```
run-fermi.pl -k 200 -p cdhitout_0.85 | make -f -
```
however `fermi` hangs indefinitely. When I look…
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Hi! I'd like to know the abundance or coverage of unitigs. I notice that GGCAT can provide such information and I'm wondering what k-mer counter is used (standalone programme or built-in programme)?
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Hi Team,
Appreciate if someone can advise me on this issue:
**Previous steps:**
1. SNP and COG association with fixed effects model
**Pyseer having issue:** K-mer association with mixed effec…