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Hello!
I run:
**reckoner -genome 4500000000 -prefix ${p} -threads 128 -kmcmemory 900 -longkmer -verbose -reuse ${r1} ${r2}** …
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I have an RNA seq that I need to assemble from PacBio and when I send the script the program do not pass the stage 2. I work with PACbio long read Hifi sequence that end up being all around 12 mil…
A-pcd updated
3 months ago
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**EDIT I guess it would help if I were to read the publication to see especially the figures on time and amplitude domains' effects on base identity.**
Hi, thank you very much for developing this t…
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Hi,
I have met with another ignoring error, here is the log:
0.982908 k-mers per position
14994 DB matches per sequence
8 overflows
0 queries produce too many hits (truncated result)
58 sequen…
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### Description of bug
I tried to assemble metagenome reads via SPAdes (--meta), yet only the first k-mer can be assembled successfully without other manipulations. During the second k-mer assembly…
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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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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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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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Currently workflow does k-mer counting on the individual fastqs from each bam, but then goes on to combine the fastq. Should k-mer counting be performed on the combined fastq or the parts?
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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:
```
…