TranscriptAssembly pipeline can be improve

NBISweden / pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.

GNU General Public License v3.0

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TranscriptAssembly pipeline can be improve #3

Open Juke34 opened 4 years ago

Juke34 commented 4 years ago

Should be more generalized. With choice for read aligner:

star
Hisat2

choice of different assemblers (Why? Because better result: ):

denovo:
- soap denovo trans
- Oases
- trinity
guided
- Stringtie
- Scallop
- Bayerassembler

And an optional filtering step at the end: Mikado
EviGene

LucileSol commented 3 years ago

we could also add normalization (as an option if data too big). do we do denovo or reference guided with trinity? (we could do both) need QC (transcript QC : detonate, transrate, more?) need filtering maybe

use scilifelab (nf-core) RNAseq pipeline? to check