ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-12-16T16:21:28+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/221[IlluminaWF] Change algo use with BWA for ContaminationSearch analysis2022-12-16T16:21:28+01:00Jules Sabban[IlluminaWF] Change algo use with BWA for ContaminationSearch analysisCurrently, the **ContaminationSearch** analysis for illumina workflows is performed with `bwa aln`.
This algorithm is not optimal for the length of reads we currently have ; so we should use `bwa mem`.
Moreover, in the future pipeli...Currently, the **ContaminationSearch** analysis for illumina workflows is performed with `bwa aln`.
This algorithm is not optimal for the length of reads we currently have ; so we should use `bwa mem`.
Moreover, in the future pipeline under Nextflow we will use ***FastqScreen*** to make this analysis. This tool already use `bwa mem`.
So to have comparable results between the two pipelines, we must change `bwa aln` to `bwa mem`.Jules SabbanJules Sabbanhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/164[Hi-C] Hi-C pipeline developpement2022-12-16T16:21:28+01:00Claire Kuchly[Hi-C] Hi-C pipeline developpementImplementation of a new pipeline that takes Hi-C data :
* [ ] Implementation new CasavanG6workflow illumina_HiC_qc
* [ ] Implementation of juicer analyse - must make available the file merge_nodup.txt
* [ ] Implementation of juicer re...Implementation of a new pipeline that takes Hi-C data :
* [ ] Implementation new CasavanG6workflow illumina_HiC_qc
* [ ] Implementation of juicer analyse - must make available the file merge_nodup.txt
* [ ] Implementation of juicer result (file inter.txt) interface with smartyClaire KuchlyClaire Kuchly2020-04-30