tderrien/manopore

Manopore

Manopore is based on Nanoseq which is a bioinformatics analysis pipeline that can be used to perform basecalling, demultiplexing, mapping and QC of Nanopore DNA/RNA sequencing data. Nanoseq v1.1 also perform a reference-guided transcript discovery and quantification using bambu.

Usage

1. Add at the top of sbatch_launcher.sh:

   • The directory where your fast5 are located.
   • The sample id.
   • The reference annotation and genome.
   • The Flowcell ID and the kit.
   • The protocol (cDNA, directRNA, DNA)

2. Everything is done on your side. Now, Manopore will automaticaly create the input files, run Nanoseq on GPU, and put a Quality Check online (NanoPlot).

Outputs

At the end of Manopore, you will find :

• The fastq.gz file created by guppy.
• All the Quality Control done by PycoQC, NanoPlot, MultiQC.
• The sorted BAM file computed by minimap2
• BigWig and bigBed for visualisation.
• Transcript reconstruction and quantification (bambu).

Issues

At the moment (Dec 2020), it presents a problem (see issue), and has to be used in two steps. (04/01/20 : Should be fixed in the next release)