metagWGS issueshttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/issues2022-12-02T15:09:30+01:00https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/issues/201Improve HiFi binning2022-12-02T15:09:30+01:00Ghost UserImprove HiFi binningDifferent possibility to improve HiFi binning:
* Implement a circular aware startegy as in the [Binning Pacbio Pipeline](https://github.com/PacificBiosciences/pb-metagenomics-tools/blob/master/docs/Tutorial-HiFi-MAG-Pipeline.md). Check o...Different possibility to improve HiFi binning:
* Implement a circular aware startegy as in the [Binning Pacbio Pipeline](https://github.com/PacificBiosciences/pb-metagenomics-tools/blob/master/docs/Tutorial-HiFi-MAG-Pipeline.md). Check on project if it would really improved the results
* Use of assembly graph: information of the assembly graph could be used to bin contigs : Check [RepBin](https://github.com/xuehansheng/RepBin), [https://github.com/metagentools/GraphBin2](GraphBin2), [GraphMB](https://github.com/MicrobialDarkMatter/GraphMB)
* Use of methylation marks found in HiFi reads : check [nanodisco](https://github.com/fanglab/nanodisco) use to do that with ONT reads. The methods was originally made for PacBio RS II data with the tool [mbin](https://github.com/fanglab/mbin). It is now possible to call methylation in HiFi reads so we could theoretically apply this method with our HiFi reads.Issues en vrachttps://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/issues/143Replacing alignment methods with quantification methods (kmer...)2021-06-28T16:03:14+02:00MARTIN PierreReplacing alignment methods with quantification methods (kmer...)Instead of aligning sequences throughout all the pipeline, should we:
- Replace those operations with non-alignment methods (quantification) or pseudo-mapping (through kmers)?
- If so, what to use? Salmon/CD-HIT/other?
Evaluate impact o...Instead of aligning sequences throughout all the pipeline, should we:
- Replace those operations with non-alignment methods (quantification) or pseudo-mapping (through kmers)?
- If so, what to use? Salmon/CD-HIT/other?
Evaluate impact on pipeline, output files format (and "CO2 emissions" as less alignment means less work on the cluster).