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It would be nice with some simple examples on how to generate the most basic input data: assembly + coverage
## Estimate the amount of data you need
(100%/target_abundance%) * average_genomesize *…
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Maintain information about the length of contigs and calculated expected coverage, using this, add a -e switch to Newbler (Spades doesn't seem to support expected coverage, but research this further).…
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Different dataset with exactly same parameters set, sometimes I got error message as below, but still get a `contig.fa` file.
`terminate called after throwing an instance of 'std::logic_error' what…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.1.5
**To Reproduce**
Exact bcbio command you have used:
```
bcbio_nextgen.py {CONFIG_YAML} -t ipython -n 41 -s sge -q main.r…
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Have run the test packaged with the software successfully. But when I try to run my own data, I get the following error:
python create_inference_graphs.py --reads All+RatQ3.fastq --gfa raven-unpoli…
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Hi there,
I am using GenomeScope2 to check the heterozygosity rate of a plant genome (2n=28) with HiFi reads.
The initial assembly with Hifiasm was used for running a mummerplot with A. thalian…
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Hi,
Been running the pipeline and get the following error for FRCBAM and REAPR, however I'm mostly interested in REAPR and can't quite find out the problem. It is installed in Utilities/cpp/Linux-x…
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When bioboxes/rfc#204 in completed, the bioboxes file validator should check
that the mandatory metrics file is produced by the assembly validator.
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We've had reasonably good results with [IVA], but it has a few problems:
1. Some samples are very slow, even taking multiple days. Random primers seem to be slow.
2. We find contigs with a lot of …