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I have some metatranscriptomic data and I want to run it through ARGs-OAP, is this reasonable?
If not, any other suggestions would be greatly appreciated.
Thank you so much for taking the time to re…
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Seqspec (https://github.com/IGVF/seqspec) is a machine-readable specification for libraries, a file format based on yaml, that enables sequence read annotation. The scope is broader than ours, includi…
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@sandraTriebel see here a nice guide for Nanopore/ hybrid genome assembly:
https://achri.blogspot.com/2019/12/nanopore-bacterial-genome-assemblies.html?m=1
Whereas here the focus is fast executi…
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```
I looked trough the sources in truck and figured out that bwa_seq always do
'aln' followed by 'samse'. Do you have any plans to implement also paired end
alignment method ('sampe'). We have Illu…
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If I attempt to use --input-fmt-option nthreads=4 when opening a BAM file it tells me it cannot open the file.
```
@ seq3c[samtools.../samtools]; ./samtools calmd --input-fmt-option nthreads=4 /tmp/N…
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```
Hi,
I use cutadapt to trim Illumina reads for adaptor sequences and low-quality
bases. I would love to also have the option to filter out reads that fail the
Casava 1.8 filter ("Y" in sequence i…
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```
Hi,
I use cutadapt to trim Illumina reads for adaptor sequences and low-quality
bases. I would love to also have the option to filter out reads that fail the
Casava 1.8 filter ("Y" in sequence i…
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`split_libraries.py` has the `-j` option which allows you to deal with duplicated barcodes across different "runs/lanes", however `split_libraries_fastq.py` does not include this option.
One of the t…
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### Description of feature
This is related to https://github.com/nf-core/demultiplex/issues/81, which states (but is not the main concern of the linked issue)
> Also `https://raw.githubusercontent…
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A colleague wrote:
>Not sure if it is of interest, but PRJEB49093 has 151 M. tuberculosis isolates with matched Illumina and Nanopore data. Mixture of resistance profiles.
>The raw nanopore data a…