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Hi @freeseek
Following up on #68, I was wondering if it may be feasible for you to include an Illumina_genotype tag in the FORMAT field? I see that based on ALLELE_A/ALLELE_B and GT the illumina_g…
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This code
```console
nextflow run fmalmeida/ngs-preprocess -r dev -latest -profile docker --sra_ids "./input/sra_ids.txt" --output illumina_single --shortreads_type "single" --fastp_addit…
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### Description of feature
Hi,
Illumina has introduced a new read compression format, ORA: https://www.illumina.com/science/genomics-research/articles/design-ora-lossless-genomic-compression.htm…
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### Description of the bug
I know it is still work in progress, but the new version of this pipeline `https://github.com/nf-core/rnavar/tree/dev` seems really promising. However, it only takes the fi…
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Try
```python
# Initialise the API client
with ApiClient(get_icav2_configuration()) as api_client:
# Create an instance of the API class
api_instance = BundleDataApi(api_client)
try:…
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I have nanopore long-reads from tumor (tumor only)
I also have SNP/indel variant calls from the same sample from illumina in both germline (normal) and tumor data
I want to try and phase the tumou…
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Dear author,
Thanks for this pipeline! I am using this pipeline with a mammalian species. I would like to launch the workflow using illumina and nanopore data together. Is it valid to use -sr and -lr…
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https://www.youtube.com/watch?v=fCd6B5HRaZ8
https://www.youtube.com/watch?v=-7GK1HXwCtE&list=PLnzAhaRtwW9cpQjk7IMj6gGq7UMPOKuq9&index=1
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I note that [SAMN00205533](https://www.ebi.ac.uk/ena/browser/view/SAMN00205533) is not in the assembly-stats.tsv file. It's isolate (culture) sequence from the E. coli Long Term Evolution Experiment. …