Jacques Dainat
Subsampling only takes top n reads in .fastq files. Can be improved by selecting reads randomly.
Hello, I found that from the CRG: https://github.com/biocorecrg/GeneidTRAINerDocker you might train this other abinitio tool, prediction can be done aside and result provided for reconciliation via MAKER or EvidenceModeler.
@Mahesh You already mentioned the [FA-nf pipeline](https://github.com/guigolab/FA-nf), might be a good alternative to ours. They would like to reimplement it in DSL2 maybe we could join our efforts and create...
Should be more generalized. With choice for read aligner: - star - Hisat2 choice of different assemblers (Why? Because better result: ): * denovo: - soap denovo trans - Oases...
See #17 for the general picture. The purpose of this pipeline is to generate gff alignment from protein or transcript fasta files. Those gff must be formatted in match match/part...
See #17 for the general picture. The purpose of this pipeline is simply to run MAKER. MAKER can be run to make evidence annotation, abinitio evidence-driven annotation or only as...
See #17 for the general picture. Maybe can be merge with the DeNovoRepeatLib pipeline (see #32). The purpose of RepeatMaskMyGenome is to repeat mask a genome based on a repeat...
See #17 for the general picture. Maybe can be merge with the DeNovoRepeatLib pipeline (see #33). The purpose of DeNovoRepeatLib is to make de-novo repeat library of a genome. There...
See #17 for the general picture. The idea of this pipeline is to parallelise PASA to make it faster to run. Having PASA would be nice because it can be...
See #17 for the general picture. Here a description of the AnnotationToENA pipeline we need: Input file: 2 => The GFF file along with the Fasta file Tool needed: AGAT,...