GenomiqueENS/nf-workflows

nf-workflows

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

1. Define input section of nextflow.config file:

   • Nanopore data
   • Genome annotation
   • Illumina short reads (optional)

2. Read orientation (Eoulsan)

3. 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)

4. Isoquant subworflow

   • Mapping reads to genome (minimap2)
   • Convert sam to bam files (samtools)
   • Concatenate bam files into single bam (samtools)
   • Transcript annotation (Isoquant)