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Hi everyone I am new to MaSuRCA Reference guided assembly. I am using chromosome_scaffolder.sh for scaffoding. I have shared the log info, I don't know what is the error. Could you help me with this?
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Hello, I'm trying to run a multiple genome alignment with the following parameters:
```
runProgressiveCactus.sh SEQUENCE_FILE_v2.txt ./CACTUS_v2 ./Chlorophyta_v2 \
--maxThreads 20 --root Chlo…
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This is a feature request/enhancement (tangentially related to issue #60).
I was wondering if there are plans to incorporate --junc-bed and --junc-bonus parameters in Miniprot, similar to the curre…
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I assembled two haplotype-resolved T2T genomes. When I followed your suggestion to set the parameters and combined the two haplotype genomes into a single FA file for evaluation using GCI, the score w…
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Hi,
I have a set of paired-end reads from bacterial RNA. Since the reference genome I'm using has a gene that's overlapping between the beginning and the end of the chromosome, I was wondering how ST…
EBosi updated
3 years ago
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Dear AnchorWave team,
I am currently working on a project that involves calculating identities of 1M window size pairwise alignments in whole genome comparisons. I understand that AnchorWave is des…
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Hello！I runed this code `bash /Bio_data/zzy/software/MUMandCo/mumandco_v3.8.sh -r common_carp.genome.chr.fin.fasta -q C.auratus.chromosome.chr.fasta -g 1531013968 -t 10 -o sv`.But after running it for…
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In some cases, I believe that the "View chimeric alignments in split screen" feature is zooming to the wrong endpoint on the supplementary read. Here is an example:
![chimeric_view_error](https://g…
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When comparing with Cactus, how to call the GPU? Why did I use the -- GPU 1 command and run it successfully, but it didn't show that the GPU was called
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## Short description of the problem
Even in single-contig circularized genomes, `anvi-run-hmms` does not reliably detect the 5S rRNA gene.
## anvi'o version
```
Anvi'o ......................…