ONT_pilot_gitlab issueshttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues2021-03-25T08:27:40+01:00https://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues/122Manuscript: discovery of novel taxa in GDB2021-03-25T08:27:40+01:00Valentina Galatavalentina.galata@uni.luManuscript: discovery of novel taxa in GDBOne of the preprocessing steps was to remove rRNA reads from metaT data using `bbduk`.
However, this step did not remove reads demonstrarting a certain level if dissimilarity to the used references.
Some rRNA genes have a rather high met...One of the preprocessing steps was to remove rRNA reads from metaT data using `bbduk`.
However, this step did not remove reads demonstrarting a certain level if dissimilarity to the used references.
Some rRNA genes have a rather high metaT coverage and that can be used to find "novel taxa", i.e. those not covered by the used rRNA references.Stretch goalhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues/126Analysis: metaT cov w.r.t. gene length2021-03-25T08:27:18+01:00Valentina Galatavalentina.galata@uni.luAnalysis: metaT cov w.r.t. gene lengthMetaT coverage of CDS of proteins should be also computed w.r.t. sequence length, i.e. how much of the transcript is covered.MetaT coverage of CDS of proteins should be also computed w.r.t. sequence length, i.e. how much of the transcript is covered.Stretch goalhttps://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.luhttps://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/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/117Binning - methylation vs non-methylation2021-01-14T08:39:41+01:00Susheel BusiBinning - methylation vs non-methylation- Hypothesis: `methylation status does not affect binning, especially for bacteria`
- To be tested in the future.
- Previous `binning` folders from methylation-aware and non-methylation-aware basecalling stored on the `work` folder for ...- Hypothesis: `methylation status does not affect binning, especially for bacteria`
- To be tested in the future.
- Previous `binning` folders from methylation-aware and non-methylation-aware basecalling stored on the `work` folder for reference and useStretch goalSusheel BusiSusheel Busihttps://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/52Assembly w/ metaT2020-11-03T12:10:03+01:00Valentina Galatavalentina.galata@uni.luAssembly w/ metaT* [ ] polish w/ `racon`
* [ ] assembly w/ `rnaSPAdes` and merge with SR/hybrid assemblies w/ `???`
* [ ] assemble w/ `???` using SR/hybrid assembly as "trusted contigs"* [ ] polish w/ `racon`
* [ ] assembly w/ `rnaSPAdes` and merge with SR/hybrid assemblies w/ `???`
* [ ] assemble w/ `???` using SR/hybrid assembly as "trusted contigs"Stretch goalhttps://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/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/33Plasflow: hybrid vs. SR assembly2020-07-03T13:22:41+02:00Valentina Galatavalentina.galata@uni.luPlasflow: hybrid vs. SR assembly- Does the hybrid assembly help to characterize unclassified contigs from the SR-only assembly?
- Do longer contigs allow for better chromosome/plasmid prediction?
[See also this comment](https://git-r3lab.uni.lu/susheel.busi/ont_pilot_...- Does the hybrid assembly help to characterize unclassified contigs from the SR-only assembly?
- Do longer contigs allow for better chromosome/plasmid prediction?
[See also this comment](https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/issues/30#note_50684)Stretch goalhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues/5Non-mod data: Gene/protein analyses2020-06-10T07:30:08+02:00Susheel BusiNon-mod data: Gene/protein analyseshttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/issues/14Flye-binning2020-06-07T12:57:20+02:00Susheel BusiFlye-binning- Chunkify 'flye' assembly and run through BusyBee- Chunkify 'flye' assembly and run through BusyBeeSusheel BusiSusheel Busi