ONT_pilot_gitlab issueshttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues2020-09-18T07:26:22+02:00https://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues/85Alternative tools for gene calling2020-09-18T07:26:22+02:00Valentina Galatavalentina.galata@uni.luAlternative tools for gene callingConsider to use other tools for gene calling besides `prodigal`Consider to use other tools for gene calling besides `prodigal`Stretch goalValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues/94Analysis: Comparing assemblies: SibeliaZ2020-11-10T11:41:45+01:00Valentina Galatavalentina.galata@uni.luAnalysis: Comparing assemblies: SibeliaZAdd `SibeliaZ`
- [repo](https://github.com/medvedevgroup/SibeliaZ)Add `SibeliaZ`
- [repo](https://github.com/medvedevgroup/SibeliaZ)Stretch goalValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues/99Annotation/Analysis: FAMLI2020-10-19T09:54:02+02:00Valentina Galatavalentina.galata@uni.luAnnotation/Analysis: FAMLIFAMLI = Functional Analysis of Metagenomes by Likelihood Inference
an algorithmic approach to correctly assign aligned WGS reads to the proper reference sequence
- [paper](https://bmcbioinformatics.biomedcentral.com/articles/10.118...FAMLI = Functional Analysis of Metagenomes by Likelihood Inference
an algorithmic approach to correctly assign aligned WGS reads to the proper reference sequence
- [paper](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03802-0)
- [repo](https://github.com/FredHutch/FAMLI)Stretch goalhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues/113Prodigal benchmark2021-01-19T09:07:17+01:00Valentina Galatavalentina.galata@uni.luProdigal benchmarkCompare `prodigal` predictions to a ground truth.
Use a couple of genomes from NCBI to run `prodigal` on a FASTA of concatenated genomes and compare the predictions to the genome annotations (GFF files).Compare `prodigal` predictions to a ground truth.
Use a couple of genomes from NCBI to run `prodigal` on a FASTA of concatenated genomes and compare the predictions to the genome annotations (GFF files).Susheel BusiSusheel Busihttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues/115Error: segmentation fault for hmmsearch (rumen/aquifer, LR assemblies)2021-01-19T09:07:25+01:00Valentina Galatavalentina.galata@uni.luError: segmentation fault for hmmsearch (rumen/aquifer, LR assemblies)`hmmsearch` using KEGG HMMs crashes with "Segmentation fault" for `rumen` (`flye`, `raven`) and `aquifer` (`flye`).`hmmsearch` using KEGG HMMs crashes with "Segmentation fault" for `rumen` (`flye`, `raven`) and `aquifer` (`flye`).Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues/116Error: assembly alignment error in mummer/dnadiff (rumen, LR assemblies)2021-01-19T09:07:29+01:00Valentina Galatavalentina.galata@uni.luError: assembly alignment error in mummer/dnadiff (rumen, LR assemblies)`dnadiff` aborts with an error for `flye` and `raven`
```
Building alignments
ERROR: failed to merge alignments at position 30798
Please file a bug report
ERROR: Failed to run nucmer, aborting.
````dnadiff` aborts with an error for `flye` and `raven`
```
Building alignments
ERROR: failed to merge alignments at position 30798
Please file a bug report
ERROR: Failed to run nucmer, aborting.
```Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.lu