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Is there a way to kmer query a spacegraphcat to label all the kmers by their partition? I am trying to use spacegraphcat for kmer partitioning.
@ctb suggested `kmer,cdbg_id,level1_domset_id` as an …
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Hello,
I'm trying to use the STAT tools to build a database from fasta sequences, and then using it to do metagenomics/taxonomic analyses.
So I'm following the tutorial in the build_db_and_run.sh …
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张老师 您好!
判断超大基因组(50G)是否为异源或者同源染色体,集群内存5T,
最近运行总是报错,运行命令如下:
`subphaser -i part1.fasta -c new_1.config -lower_count 3 -pre Al_out > Al.log`
报错信息如下:
`24-08-06 23:49:35 [INFO] Filtering differential …
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Hi, I found the pangenie-index calculate the unique kmers in the variant flank sequences, so could you please tell me what the unique kmers are used for pangenie genotyping?
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I think there could be an argument to merge them into one iterator.
We may need to benchmark, but,
The current iteration implementation for EveryKmer when the kmer-longseq alphabets match is:
```…
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Hi, I am trying to run on a large amount of samples (900M reads).
command:
`Trinity --seqType fq --max_memory 50G --left all_1P.fq.gz --right all_2P.fq.gz --SS_lib_type RF --CPU 16 --no_salmon`
T…
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Currently, one can't make 0-length kmers:
```
julia> DNAKmer(dna"")
ERROR: ArgumentError: Bad kmer parameterisation. K must be greater than 0.
Stacktrace:
[1] checkmer(#unused#::Type{DNAKmer{0…
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Hello,
Many users of PanGenie might wish to use vg giraffe to align reads for short-variant calling, but use PanGenie for structural variant calling.
Inspired by PanGenie, the new haplotype-bas…
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Rethinking regarding the chunk size, should we define the chunk size as the number of sequences or the number of kmers?
Chunk size as the number of sequences should work when the sequence lengths a…
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I have a question, how to set parameters to assemble long fragment repeats like rDNA using hifiasm? Why the max kmer can only go to 63, like verkko high k-mer sizes to construct a multiplex de Bruijn …