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Hi,
I was trying `GraphAligner` to error correct some PacBio CLR reads using a non-standard graph that I made with `prophasm` using it's simplitigs concept (https://github.com/prophyle/prophasm) in…
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Hi,
I have used canu (2.0) to assemble an insect genome with high (>1%) heterozygosity from Pacbio CLR data. I used the recommended batOptions for assembling both haplotypes separately.
`canu -a…
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ABySS 2.2.5
What does `Different` in the log file mean regarding read mapping/orientation? What is their origin?
Like here:
```
Mateless 0
Unaligned 193071 0.106%
Singleton …
ms-gx updated
3 years ago
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Hi there,
I see that Canu v2.1.1 does not report unitigs in fasta format like previous versions. Is there a way to generate this file for special cases? In my experience, contigging (using CCS data…
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Greetings of the season.
Here is the history of my installation process.
```
conda create -n SALSA python=2.7 #Create the SALSA environment and install python 2.7
source activate SALSA #Act…
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Hello,
Thanks for this very useful tool. One lacking feature (or perhaps I could just not find it?) is that there is no coverage depth information available in the GFAs produced. Is there a way to ac…
jflot updated
3 years ago
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The graph of wtdbg2 is given by a .dot file, but it does not relate the reads to the edges. Currently we relate much less reads to edges than we apparently could, looking at the unitigs. We need to fi…
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```
rule make_contigs_kmer_index:
input: rgnv_nbhd_k31/bcalm.unitigs.db
output: rgnv_nbhd_k31_r5/contigs.mphf, rgnv_nbhd_k31_r5/contigs.indices
jobid: 2
/home/tereiter/m…
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Hello there,
Thanks for developing such wonderful tool. There is an idea that I want to test.
I would like to know if the resulting haplotype-specific assembly from hifiasm using '-3 -4' is better …
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Trying to annotate significant unitigs.
I annotated a genome (complete) using prokka then used the fasta and gff with annotate_hits_pyseer
this works and the script runs ok but there are no gene…