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See https://github.com/pmelsted/GFA-spec
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Hey guys!
So, I'm trying to correct my PacBIo DNAg reads, and I have about 70x coverage with Illumina short reads. But the thing is this set is divided between 180pb that can be merged, and 500bp tha…
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Running proovread in mr+dazz-utg mode I faced with error at mapping unitigs stage.
The problem turned out to be in short fragments from utg file provided as input.
This can be simply resolved with @t…
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Dear Heng,
Looks like a great tool and I tried to use it for a subset of the Anopheles 1000 Genomes data (https://www.malariagen.net/apps/ag1000g/phase1-AR3/index.html).
The first problem I encounter…
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I'm looking for failing unitig/contig alignments.
Reads past `-B` bases in length are aligned in "banded" mode in which the read is broke into overlapping subreads, each subread is mapped independen…
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I'm running `vg map` on some paired-end reads now, appears to be going smoothly.
I'd previously tried it on some @lh3 fermikit unitigs and hit the following:
```
$ time vg/vg map -f mlin_unitigs.ma…
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@ekg @jltsiren I made a run at the [xg/GCSA2 whole genome indexing](https://github.com/ekg/vg/wiki/working-with-a-whole-genome-variation-graph) and got the aforementioned error from build_gcsa. I see …
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I am restarting calculations from version 1.0.2 now with version 1.0.3.
Is it possible that the relase 1.0.3 is tackling the "Error 9", which I had several times to fight with in a 17 Samples assembl…
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Probably a novice roadbump: I have `11.vg` for the whole chromosome and I'd like to extract a subgraph and then align a sequence to it. Based on [05_vg_find.t#L32](https://github.com/ekg/vg/blob/faa5e…
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is it possible to change the ploidy for the variant calling steps (can't see a flag)?