nemADSQ

A repository containing pipelines for nematode genome assembly, decontamination, scaffolding, and QC.

Requirements

Most requirements will be satisfied automatically by nextflow using the conda environment specification, but requires Red (REpeat Detector) which you can get http://toolsmith.ens.utulsa.edu. Install one of the pre-built binaries for your system or build from source. The Red executable needs to be in your $PATH.

Example run

# clone the repo
git clone https://github.com/tolkit/nemADSQ.git

# To install nextflow
wget -qO- https://get.nextflow.io | bash
# if no java found by nextflow:
# sudo apt install openjdk-8-jre-headless

# Get Red
wget http://toolsmith.ens.utulsa.edu/red/data/DataSet2Unix64.tar.gz
tar zxf DataSet2Unix64.tar.gz 

# add new binaries to a local bin directory
mkdir bin
export PATH=$PWD/bin:$PATH
mv nextflow redUnix64/Red bin/

# Download data
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/067/145/GCA_904067145.1_BOKI2/GCA_904067145.1_BOKI2_genomic.fna.gz -O B_okinawaensis.fasta.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR243/DRR243689/DRR243689_1.fastq.gz -O B_okinawaensis.npr.fasta.gz

# Run pipeline
nextflow -C nemADSQ/qc_assem.conf run nemADSQ/qc_assem.nf --assemblies "B_okinawaensis.fasta.gz" --reads "B_okinawaensis.npr.fasta.gz" --busco2nigons nemADSQ/example/gene2Nigon_busco20200927.tsv.gz

Example result of Bursaphelenchus okinawaensis (GCA_904067145.1) assembly.

Troubleshooting

If the fraction of repeats appears to be 100% all along the sequences, the bedtools version is incompatible. Check which bedtools is available from the terminal where you launched nextflow and upgrade to bedtool>=2.30.0.