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I am assembling a two genomes independently with the following script:
spades.py -k 21,33,55,77,99,127 --careful -1 trim_SCLB_R1_paired.fq.gz -2 trim_SCLB_R2_paired.fq.gz -o spades_assembly
wit…
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Hello！
I am using The Minigraph-Cactus Pangenome Pipeline to construct the pan-genome of pigs. I know that different pan-genomes can be obtained by setting the value of the parameter `filter` in…
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Hello,
We are currently using kraken2+bracken but would definitely want to use the advantages of krakenuniq to identify unique kmers to reduce false classification.
I came across this [publication](…
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Hello,
I am using spades v3.14 in `--meta` mode. I got an error, these are the last lines in the log file:
```
2:34:39.146 46G / 105G INFO StageManager (stage.cpp …
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Presented the ChIP-seq peaks vs flanks comparison on Friday ENCODE call today. Jeff and Jacob suggest that HashingVectorizer is not a good comparator for my method since I want something that takes p…
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e.g. Input parameter is set to `--num_splits 12` but only 8 contigs are in the input
```
Error executing process > 'AUTOMETA:PRODIGAL (Annotating mock_metagenome)'
Caused by:
Process `AUTOME…
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@marekkokot Is there a test suite you use to verify correctness of kmc and kmc_tools? If there is, could it be checked into github?
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Hi.
When I performed a de novo assembly using HIFI, I obtained a genome size of 1.7 Gb. Since there was no prior information available about my sample, I decided to estimate the genome size. When …
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We have a lot of training materials not listed here from DIBSI and other workshops outside of UCD. Wanting to share these materials with others (like people who come to MAD), but have to go hunt them …
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Hi,
I am trying to build a database from RefSeq and GenBank genomes.
The total size of the ~1.9 million compressed genomes is ~8.5T. Since the data set contains many genomes, some of which with ex…