output.md

Outputs

This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.

Pipeline overview

The pipeline is built using Nextflow and processes the data using the steps presented in the main README file.
Briefly, its goal is to generate ready-to-use annotations for downstream analysis pipelines.

The directories listed below will be created in the output directory after the pipeline has finished.

genome

The genome folder contains everything about the assembly itself, with :

• The genome in fasta format (.fa, .fas, .fasta)
• The genome index file (.fa.fai)
• The genome dict file (.dict) mainly for GATK usage
• The chromosome size file (.sizes)
• The effective genome size defined by the sum of non 'N' base on the genome (.effgsize)

indexes

The current version of the pipeline allows to automatically generates indexes for the following mappers ;

• STAR
• bowtie2
• bwa
• hisat2

gtf

The gtf folder contains the annotations files generated from gtf or gff files, with :

• The complete annotation in gtf/gff format (.gtf)
• The annotation in bed12 format, usefull for some tools like rseqc
• The gene-based annotation in bed format
• If available, all these files are also created for protein coding annotation only, using the keyword gene_type or gene_biotype