CANU

CANU (genome assembly)

• Author: Dreycey Albin
• Date: DATE 05/07/2019
• A program for genome assembly using single molecule sequencing data
• Oxford Nanopore or Pacbio
• documentation (website): https://github.com/marbl/canu
• documentation (publication): https://genome.cshlp.org/content/27/5/722
• quick start guide: https://canu.readthedocs.io/en/latest/quick-start.html#quickstart
• detailed start guide: CANU FULL TUTORIAL

Installation

git clone https://github.com/marbl/canu.git cd canu/src make -j 3

Basic commands

canu [-correct | -trim | -assemble | -trim-assemble]
[-s ]
-p
-d
genomeSize=[g|m|k]
[other-options]
[-pacbio-raw | -pacbio-corrected | -nanopore-raw | -nanopore-corrected] *fastq

• can correct, read, and trim separately:

• correct

canu -correct \
  -p ecoli -d ecoli \
  genomeSize=4.8m \
  -pacbio-raw  pacbio.fastq

• read

canu -trim \
  -p ecoli -d ecoli \
  genomeSize=4.8m \
  -pacbio-corrected ecoli/ecoli.correctedReads.fasta.gz

• assemble

canu -assemble \
  -p ecoli -d ecoli-erate-0.039 \
  genomeSize=4.8m \
  correctedErrorRate=0.039 \
  -pacbio-corrected ecoli/ecoli.trimmedReads.fasta.gz

INPUT

GENERAL INPUT INTO PROGRAM (files and commands)

OUTPUT

GENERAL OUTPUT FROM PROGRAM (files and commands)

Example_1- assemble a low coverage genome

• stolen from the reference manual

curl -L -o yeast.20x.fastq.gz http://gembox.cbcb.umd.edu/mhap/raw/yeast_filtered.20x.fastq.gz
gzip -d yeast.20x.fastq.gz;

Input files

nanopore reads

Output files

Genome assembly files

Download nanopore data

• Download E. Coli nanopore run from https://www.ebi.ac.uk/ena/data/view/ERX708228

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR764/ERR764952/ERR764952_1.fastq.gz;
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR764/ERR764952/ERR764952_2.fastq.gz

convert nanopore fastq files to fasta

cat ERR764952_1.fastq | paste - - - - | sed 's/^@/>/g'| cut -f1-2 | tr '\t' '\n' > NANOPORE_INPUT.fa

commands

./Darwin-amd64/bin/canu  -p albinout -d pairedout  genomeSize=4.8m  -nanopore-raw Nanopore_TB.fa