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in the `bcalm_to_gxt` step, some nodes are removed & merged with others in order to simplify the graph. during the ensuing indexing of k-mers, it looks like the k-mers that belong to these removed nod…
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Hi,
Now that contigs.gfa got removed, is there another file that gives you the CIGAR string of the self-alignment to identify trimming points for circular contigs?
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hi folks, the bug we reported for Linux in #37 and #44 is baaaaaack! but this time for Mac OS X!
briefly, bcalm is producing a cDBG where there are links that are not bidirectional.
full details…
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What does the output below mean.
```shell
cd unitigging
/public/canu_v2.0/Linux-amd64/bin/tgStoreDump \
-S ../out.seqStore \
-T ./out.ctgStore 2 \
-sizes -s 1900000000…
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Hello John,
When I was reporting another issue (fixed rev-comp problem with unitig-caller), I've realized unitig-counter seems to make erroneous calls if a contig in particular isolate starts with…
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Hi,
I have to confess that I have only used `Ratatosk` once, but I was just thinking about the option for "trimming". The program `GraphAligner` (https://github.com/maickrau/GraphAligner) offers so…
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I am using PILON To correct a 500M genome assembly obtained from CANU+Quiver. I have
2,190,431,976 reads in sorted.bam file (should guarantee about 300x coverage). When I start PILON, it reports a ne…
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Hi Guillaume,
I am running Bifrost built from source (26746a1), and successfully build a gfa file containing several human assemblies. For "playing around", I want to query that graph with annotated …
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Hi,
It appears as though the unitig output from `bcalm2` is very similar to the unitig output from `minia` 3.2.1. If one uses the same k-mer values and abundances, are the results about the same?
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I've encountered a potential issue in the presence/absence matrix .tsv produced by Bifrost query mode. When using multiple threads (>1), I've found some rows in the .tsv are merged with the row above …