GraphAligner
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maickrau
Hi, Thanks for the clear documentation and awesome tool. I would like to get the unique matching path for each read.But through the following code, I saw that in the...
Hi Mikko, Does GraphAligner only permit alignments that use **L** (link) lines to connect segments? or will it also report paths where a read aligns across two contigs that are...
Hi Mikko, Do you have a method to convert the graph alignment for a single read into a [GFA Path line](https://gfa-spec.github.io/GFA-spec/GFA1.html#required-fields-5)? I want to visualise individual read alignments in Bandage.
I am using a blunted assembly graph from short reads that contains several paralogs. I am aligning a long read to the graph that should partially match several paths on...
I noticed the new parameters `--diploid-heuristic` and `--diploid-heuristic-cache` in the new version of GraphAligner. This looks like a super cool feature and I'm excited to try it out - but...
Incorrect alignments, assertion errors with --seedless-DP when read has a mismatch in the first base
Occurs in v1.0.17b and master. Here is a MRE I generated with synthetic data. The ground truth segments have only ATs. I generate reads in random orientations spanning the graph...
Hi, Putting this here in case it helps anyone. When I run `micromamba env create -f CondaEnvironment_linux.yml` (adapted from the compilation instructions, using micromamba instead of conda), I get an...
Hello, I recently wanted to use Graphaligner to align the sequences of hg002 back to the GRCh38 Graph (Minigraph-cactus) released by hprc. During the process, I encountered the following issues...
Hi, I'm trying to align an assembly to minigraph cactus using the command below. However I get the following error: GraphAligner -g hprc-v1.1-mc-chm13.gfa -f XXX.fasta.gz -a {output} -t 24 --...
Hi, I tried to use GraphAligner(GraphAligner -g CPC.HPRC.Phase1.CHM13v2_Non-W.gfa -f /HJ.stLFR_CCS.maternal.fasta.gz -a aln.gam -x vg), But I got several errors message.Can you give me some suggestions. 
