Comments (2)
tseemann
commented on June 22, 2024
1
If you can assemble it with Spades, you can assemble it with Shovill.
Fungus up to 50 Mbp should be ok.
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andersgs
commented on June 22, 2024
No idea. But we would love to hear your experience with it. You may have to fiddle with RAM, though. I would say there are likely better assemblers for these larger genomes. Check out the Assemblathon 2 paper here for some ideas.
Good luck, and if you do try shovill with fungus, please let us know.
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Related Issues (20)
- Impact of giving genome size instead of estimating it from reads ?
- Pilon memory config error
- [shovill] Assembly failed - spades.fasta has zero contigs! HOT 1
- Resulting contig is way longer than expected
- Spades finished abnormally, OS return value: 21
- Error
- Error 256 HOT 2
- Confusing min ram requirements
- Failed to download resource "velvet"
- Coverage information for contigs assembled by Megahit
- Shovil tool on genome assembly of staph MRSA has 5632 error
- Harishk illumina sequence
- Hsrish
- Error 256 HOT 2
- GFA files in skesa
- what fastq filetype are available to use shovill ?
- Running shovill 1.1.0 and passing the option `'--plasmid'` to spades HOT 2
- [shovill] Can't see adapter file: /usr/local/db/trimmomatic.fa
- Illegal division by zero at /usr/local/bin/shovill line 162.
- Does Shovill support bash for running multiple fastq input files
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