-
```
Hi Sam,
a conceptual question as I have never used Novoalign before. WHat is the Index
file name? Because The moidule is validated ok, but I have these errors:
-NOVO INDEX
===Pipeline Errors…
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Hello,
I was testing accelalign performance, both in terms of speed and downstream accuracy. It seems to perform quite fast, but I finding issues with downstream analysis. Some of the tools (e.g.…
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I believe that fastp would improve the current align-DNA pipeline and workflow.
fastp is an all-in-one FASTQ preprocessor. It performs read filtering, base correction, quality control, and adapter …
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When ClipBam clips one read in a pair to length 0, it properly sets that read's `0x4` "read unmapped" bitflag, and sets the remaining aligned read's `0x8` "mate unmapped" bitflag. However the remaini…
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As suggested by @jkbonfield in https://github.com/samtools/hts-specs/issues/715#issuecomment-1508097708:
> as an aside, I note you're also using MAPQ of 255 for "unavailable". Commendable, but my e…
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HMP protocol was to 'dust' reads. We should include this feature.
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ABRA version - 0.96
Platform - CentOS
command used to run ABRA
`java -Xmx4G -jar abra-0.96-SNAPSHOT-jar-with-dependencies.jar --in C26.bam --out C26.ABRA.bam --ref hs37d5.fa --targets Agilent_Nimblege…
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**Are you using the latest release?**
Yes, version 1.8.16 as installed per https://funannotate.readthedocs.io/en/latest/install.html via conda.
**Describe the bug**
Funannotate train generates a …
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Working through a dataset, I found that most of the resulting alignments only included 100K-200K sequence identifiers from the input dataset even though most of my samples have >1M sequences. Unsure o…
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Thanks for developing MOSAIK, I tried on a human dataset and get a Segmentation fault. Any hints?
Thank you!
## /home/snow/bin/MOSAIK/bin/MosaikAligner -in LID115260_MERGE1.mkb -out ../bamfiles/LID1…