This bioinformatic pipeline is used for transcript annotation of long-read sequencing data using consensus annotated transcriptome from Isoquant and RNA-Bloom tools. This workflow is written in nextflow and developped by the GenomiqueENS core facility of the Institute of Biology of the Ecole Normale Superieure (IBENS).
Main workflow
- Define input section of nextflow.config file:
- path to nanopore data
- path to genome annotation
- path to illumina short reads (optional)
- Read orientation (Eoulsan)
- RNA-Bloom subworkflow
- Concatenate fastq files into single fastq (cat)
- Transcript annotation (RNA-Bloom)
- optional polishing with Illumina short-reads
- Mapping reads to genome (minimap2)
- Convert sam to bed file (pathools)
- Convert bed to gtf file (agat)
- Isoquant subworflow
- Mapping reads to genome (minimap2)
- Convert sam to bam files (samtools)
- Concatenate bam files into single bam (samtools)
- Transcript annotation (Isoquant)
- Creation of consensus transcript annotation