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Hi,
I am currently using NextPolish for a genome in which we are looking at a particular repeat region. Now I am wondering what NextPolish does when short-reads map to multiple parts of the genome.…
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Develop a minimap2 alignment [see [docs](https://lh3.github.io/minimap2/minimap2.html)] function that uses minimap2 (installed via conda or in the PATH), we can run this so it produces a BAM file. The…
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Hi vg team!
I'm trying to use **vg giraffe for mapping very short paired-end reads (36bp) against a pangenome**.
I tried running this command line
```
> vg giraffe -M 10 -x ${panIdxPath}/$…
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Dear strobealign devs
I'm looking to replace minimap2+CoverM with strobealign for my metagenomic binning purposes. We're currently running benchmarks to see if strobealign gives as accurate results…
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Dear Authors
I am trying to map some genomic reads (nor transcriptome or RNA-seq) with medium to long size length (above 1-15 Kb). Is HISAT2 an appropriate tool to align these reads onto a referen…
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Dear Dobin,
I'm using STAR to map the Ribo-seq results to a genome. I ran the program with and without the "--twopassMode Basic" parameter, and found that by using the 2-pass mode, the alignment ra…
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Dear all,
When comparing graph genome and linear genome in short reads mapping, I found that graph genome did not improve the short reads mapping. Has this phenomenon also occurred in your side? Fu…
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Hello again! I was wondering if there was a way to disable soft clipping for alignment, or heavily penalize its use.
Im trying to find the differences in alignments between Arioc and Bowtie2, so…
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Hello,
I have some short-read genomes that were assembled via reference mapping (different references) that I would like to align to each other. I have consensus sequences with masked reference sites…
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### Description of feature
I'm noticing a lot of multi-mapping reads and those unmapped as 'too short'. Some of this is just down to the short read lengths I guess, but we should try to add some ST…