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Hello trust4,
Version TRUST4 use Output all the required fields for AIRR format https://github.com/liulab-dfci/TRUST4/pull/138
CMD
```
run-trust4 -f {params.REF1} -t 24 --ref {params.REF2} \
…
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Hello, I have a question about the `mac` parameters in the program `list_kmers_found_in_multiple_samples`.
I set `list_kmers_found_in_multiple_samples --mac 5`, but in the file `kmers_to_use.sharen…
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**1. What were you trying to do?**
Call variants with vg. I'm trying to align of paired-end illumina reads from different bird individuals to a vg graph generated with the Cactus Pangenome Pipe…
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Hi~,
I have got a whole new set of problems now:
![image](https://github.com/zhangrengang/SubPhaser/assets/34566522/3c44b738-630b-42b4-800b-42a7e8777de1)
there is abnormally few subgenome-s…
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Hi!
At the end of Step 7, I encounter this error:
============GFA DUMP STARTING============
Graph has 23455016 edges
Dumping edges
Dumping connections
============GFA DUMP ENDED============
…
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Hello,
We are running through the tutorial for the linear mixed model and are having some issues.
We downloaded the data from [FigShare](https://figshare.com/articles/pyseer_tutorial/7588832), …
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Hello, in my project I would like to just calculate the kmer counts for one side of the reads, read_1.fq.gz, for example.
And then afterwards, I would like to compare kmer.dump across samples, I wou…
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Hi again!
Just thinking about the RefSeq versus GenBank question for analysis of a metagenome (containment). Aware that Sourmash may struggle with similar genomes (ie strains) due to a smaller numb…
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I've assembled a 1.3 Gb genome with hifiasm (version 0.14 e6e6dbf), merged both haplotypes and compared the kmer content to the read kmers with kat spectra-cn.
Because of a small heterozygocity of 0.…
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I can't seem to assemble my data, 5 Mbp bacterial genome, PE reads. I've tried various `k` and `g` etc.
```
LightAssembler -k 31 -G 5000000 -t 72 /data/R1.fq.gz /data/R2.fq.gz --verbose
```
```
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