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I recently used Novoplasty to assemble the mitogenome from short read data of _Microtonus aethiopoides_ ecotypes. Although the process completed successfully, it did not produce any contigs. I initial…
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Hi,
I want to use Spades to assemble a ~40kb plasmid sequenced with Illumina Miseq (2X250nt). When I use the default option:
`spades.py -1 ../BWA/B13_vector_unmapped.R1.fastq -2 ../BWA/B13_vector_un…
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Dear Shujun,
We're using LTR_retriever to assess a genome assembly for Chrysanthemum lavandulifolium. Because the genome is very large and a single chromosome's size exceeds 300 MB. I have been ru…
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Hi, I have been using Pilon for a few genomes but recently ran into this problem. The job is killed with no other error message mid run. Here is my command: java -Xmx350G -jar pilon-1.24.jar --fix bas…
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Good morning,
I'd like to perform the multiple genome alignments among 9 different genomes. For some reasons, I'm getting the same error as #114, which seems to appear when aligning many genomes (iss…
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Dear Maxime,
This is Jianshu, a bioinformatics PhD student at Georgia Tech. I am reaching out to you to discuss the possibility of applying the protein database structure you proposed in the kaamer…
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I'm trying to sketch the [RVDB, the Reference Viral Genome Database](https://rvdb.dbi.udel.edu/). The clustered file is ~600 MB.
```
sourmash scripts manysketch C-RVDBvCurrent.manysketch.csv -o C-…
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Hi, very nice tool - well done! Any plans for supporting cram files? It looked like you are using `samtools` for handling alignments, but one would then presumably need to pass along a reference genom…
dnil updated
13 hours ago
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I have a workflow which uses kmc to count all kmers in an extremely large dataset of about 250,000 fasta files. The workflow was originally built with v3.2.1 of kmc, but stalled when I updates to v3.2…
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Hi.
I am experiencing an issue with wgsim 0.3
If I provide a human genome in fasta format everything wrks fine, however, if I provide a larger genome the program hangs indefinetly.
In particuar:
-…