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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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#### Summary:
When calling the report for specific runs with the --run_results argument, a single value for the length of alignment is given in the alignment length column. However, the lengths of th…
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Hello,
I used the canu + Polish + circlator to assembly bacterial genomes.
The largest contig in canu assembly is considered as 'suggestCircular'.
But in the circlator :
[merge circularise_de…
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Hello mahulchak,
After I run svmu with a genome with two reference genomes, the out put of **cm.lastz.txt** and **sv.lastz.txt** shows no complete chromosomes for one reference genome .
The code …
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!!! 2017-12-08 01:18:01 Doing step 20: Getting overlaps
!!! 2017-12-08 01:18:01 Running: /usr/local/bin/nucmer -maxmatch -c 40 /public/chenl/xuxz/results/circlator/mecat.merge/minimus2.ref.seq /p…
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Hello,
I want to run core gene analysis with Spine locally and also want to include gff file, I use -f for genome_files.txt which containing paths to fasta file and their coresponding gff files. It i…
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When trying to run charcoal.alignplot, I had to install PyInterval, numpy and matplotlib manually.
I also received an error message ending with
File "/home/cmatt5/miniconda3/envs/charcoal/lib/…
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I found a weird behavior of nucmer where the presence of a "NNNN" stretch in a sequence impact the matches reported for two unrelated sequences. My example case is using nucmer to compare short virus …
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Hope you can help. I run this command but didn't see any graphical output.
python find_asm_snps.py -i ./SNV19 -o ./SNV19_out/ -v -g
The output directory just has delta files. nucmer and show-snps ex…
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I'm getting this error when executing `prove`
Did I miss something?
Full report:
```
$ prove
t/compare_pseudoalign_nucmer.t .. Could not execute command /path/vcf2pseudoalignment/master-fb3c0f4522/t…