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I have used direct RNA-seq ONT long reads data. while running the rnabloom2, I got an error in the assembly step. I am not getting the reason behind it. could you help me out? I have pasted the comma…
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Hello!
I noticed on your website that there are plans to potentially incorporate unique kmer counting into Kraken2, but however, it is not currently guaranteed. Therefore, I was wondering if this …
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ref #51
Mo -
so, khmer pre-allocate the memory even there's no need for it?
titus:speech_balloon: 9 minutes ago
Yes - after all, how do you know how many kmers there are if you haven’t read t…
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See motivation: https://github.com/dib-lab/dib-lab/issues/69
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hi,@asl
my command is
'metaspades.py -1 SRR9033753.rmhost.clean.1.fq.gz -2 SRR9033753.rmhost.clean.2.fq.gz -t 20 -o output'
when I run it by SPAdes-3.14.1, the task stuck when Processing rever…
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machine: disk 512GB, RAM 750GB, 16 cores
dataset: 23Gb, 15GB
commands that I ran for 23Gb dataset:
spades.py -o $OUT_DIR/$name --only-error-correction -s $i -m 500
and here is the log:
```
…
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When running metaspades on a paired-end FastQ files with error correction enabled, `spades-hammer` process through counting the k-mers on the forward reads, but gets stuck on doing the same on the rev…
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I have an application where I need to count pairs of k-mers separated by a fixed distance. This is almost identical to K-mer counting where K=2k, the "only" change should be in the scanning step where…
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Hello, I've used SPAdes to assemble my metagenomic datasets however two of my samples are getting stuck in the exact same place repeatedly. I was able to assemble all my samples using megahit without …
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I am not sure about below details can you please confirm,
Data structure and Sorting Algo: Enhanced suffix arrays/Counting using the lcp-interval tree
Approach: In-memory
The limit of k-size : Ar…