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Is it possible to use Winnowmap to find overlaps between long reads, equivalent to "ava-ont" and "ava-pb" options of Minimap2? If not, do you plan to add this feature in the future?
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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 tried this `rna_rp4_130bps_modbases_m6a_drach_sup` model for m6a calling and aligned the basecalled reads to the reference. Seems no alignments. See the commands below:
```
/install/buttery-eel-…
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As an optional step, it would be nice if the pipeline can also run Dorado.
Example code can be found here, bc it is not so easy to make Dorado usable on different architectures (local, HPC, ...) d…
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Hello，I use minigraph for read to rGFA alignment and i got a gaf size as 4479KB
Then I used gfatools to convert the rGFA graph to linear FASTA and compared it with the same FASTQ file，Then I got a pa…
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Speed things up by changing mafft to minimal - write a re-insertion script
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Hi, I ran a PacBio chloroplast assembly with Racon in the following way:
```
source activate minimap2
minimap2 -t 8 -x ava-pb \
input.fasta \
input.fasta | gzip -1 > output.paf.gz
so…
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Hi,
The genome I was tested is ~1G (a plant genome). The command line I have used is
/Bio/Linux-src-files/JAVA/jdk1.8.0_77/bin/java LongRepMarker -r /state/partition1/WORK/Bio/Project/zja.fa -k 4…
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Hi,
Thanks for creating such great programmes!
I have a problem when trying to install the software, it stops at the Minimap2 installation, which I have anyway installed locally using conda befo…
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Hi,
Thanks for the interesting tool. The very first Minimap2 step in the Gala pipeline is throwing usage errors.
This is what my drafts file essentially looks like (paths shortened for simple…