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For assembly of metagenomic samples with HiFi reads, I ran hifiasm-meta with default parameters. The command line was as follow:
hifiasm_meta -t 32 -o asm hifi_reads.fastq.gz
But the process was e…
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Hi!
I would like to use your tool with my own reference database.
I installed using option 2 after reading through #10
```
git clone https://github.com/liaoherui/StrainScan.git
cd StrainSc…
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Hi,
I found the list missed some recent papers:
>[Multimodal Integration] [2022 Nature Biotechnology] Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
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not sure if this is baked in already, but when running many samples from the same experiment, it would be nice if the same species/strain genome representative was prioritized for each sample in the s…
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Reading in vcfs from variant callers that run on long-read bams is only part of the problem. MAVIS still needs bam files for most operations. Such bams have a few key differences from short-read ("NGS…
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@iminkin
Hi, iminkin , thanks a lot for your amazing tool, it plays a very important role in my research !
However, I got 2 problems when I did the experiment with sibeliaz to find the colinear b…
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# Allelic Variant Explorer demo
The Allelic Variation Explorer (AVE) is a web application to visualize (clustered) single-nucleotide variants across genomes.
There is a Docker image with the app…
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Dear dRep team,
This is confusing to me when using mash sketch size 1000:
def run_mash_on_genome_chunks(genome_chunks, mash_exe, sketch_folder, MASH_folder, logdir, **kwargs):
dry = kwargs.…
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Dear all,
I have been having the following issue when installing panX. I followed the steps as in the site and used miniconda as indicated.
`Traceback (most recent call last):
File "./panX.py…
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Good night!
I am having troubles in understanding at which moment I should demultiplex my samples.
As I could understand the script python demux_by_barcode_groups.py requires the “collapse_isoforms…