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I'm using getorganelle to extract mitochondrial genomes from insects. I first do an assembly using SPAdes (because we use that output for other downstream tasks anyway), and then I run get_organelle_f…
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**Is your feature request related to a problem? Please describe.**
Currently, phables takes assembly graph files only in `gfa` format.
**Describe the solution you'd like**
Add a converting step i…
Vini2 updated
8 months ago
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Hello - is `gfastats` able to convert `fastg` to `gfa`?
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After #1371 (compact De Bruijn graph work) and #1372 etc. (assembly), can we now input/output [FASTG](http://fastg.sourceforge.net/) or [GFA](https://lh3.github.io/2014/07/19/a-proposal-of-the-grapica…
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The FASTQ parsing is currently tightly coupled with spades output. Simple nodes with no intra-sequence branching fail to load. It appears this is due to shapes-specific parsing of node names and expli…
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Spades generates a FASTG format file as well as FASTA for contigs. Some users would appreciate having the FASTG contigs available to them.
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Hi,
Thank you so much for this great tool. I was hoping to use Megahit to build fasta graphs for input to SCRAPP ([https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01068-z]).…
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Dear @voutcn,
After converting the contigs from the final value of k to FastG graph format I was going to match the resulting nodes to original contigs.
Unfortunately it seems that neither of the nu…
snurk updated
4 years ago
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Hi OPERA-MS developer,
I would like to ask where I could find the assembly graph. I searched subdirectories in the output folder, but didn't find any gfa or fastg files. It looks like it was genera…
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Thank you for developing this tool!
Makeblastdb seems to fail because no plasmids could be detected (see full log below). The reason is that `./intermediate_files/ERR4163138_contigs.cycs.fasta` is …