BUSCO with singularity

Run BUSCO for nucleotide fasta files using already downloaded BUSCO lineages

Dependencies

• singularity
• nextflow

Install singularity

conda install -c conda-forge singularity=3.6.1 -y

Download BUSCO image

singularity pull docker://ezlabgva/busco:4.1.2_cv1

Configure BUSCO version and predownload dataset

Whichever version you choose, you must specify the full path of the SIF file in the configuration file (busco_nf.config, search for "container = /a/path/busco_vx.sif"). You can get images of different BUSCO versions at this link.

The pipeline also expects the lineages (groupX_odb10) to be already downloaded. To set them up, I open an instance of the BUSCO image and run it with the desired target taxonomic group (the file used for -i can be anything as all we want is the automatic download and decompression). Stop the execution after the dataset decompression.

singularity shell busco_4.1.2_cv1.sif
# Inside this image:
busco -i anyFile.txt -l groupX_odb10 --out tmp -f -m geno
#ctrl+C

Parameters

• --busco_downloads indicates the directory that busco created to download the reference datasets
• --genomes glob path that captures the assemblies you want to assess. The files should have .fasta or .fasta.gz extension
• --outdir directory where you want to save the results
• --odb comma separated string of datasets you want to assess on each of the fasta files
• -profile configuration specific to the machine where you are running the pipeline [default or farm]

Output

In the output directory you will find for each of your fasta files, the full and short tables together with the single and multicopy sequences assessed per reference set.

Executing the pipeline in the farm

Submit an interactive job. Choose a queue appropriate to the time of execution of your pipeline. Take into account that the default config submits jobs to the 'normal' queue of 12 hours execution and if the job fails it will be resubmitted into the 'long' queue.

mbMem=5000; bsub -n 1 -q long -R"span[hosts=1] select[mem>${mbMem}] rusage[mem=${mbMem}]" -M${mbMem} -Is bash

Launch the pipeline

nextflow -c /lustre/scratch116/tol/projects/tol-nemotodes/sw/nxf_pipelines/busco_nf.config run /lustre/scratch116/tol/projects/tol-nemotodes/sw/nxf_pipelines/busco.nf
		 --busco_downloads /lustre/scratch116/tol/teams/team301/dbs/busco_2020_08/busco_downloads/
		 --genomes '/lustre/scratch116/tol/teams/team301/dbs/fasta_genomes/insects/*fasta.gz'
		 --outdir /lustre/scratch116/tol/teams/team301/users/pg17/busco_insects_renamed/
		 --odb insecta_odb10,endopterygota_odb10
		 -profile farm

nemachromQC

To assess the quality of chromosome level nematode assemblies using HiFi reads, you can use the qc_assem.nf pipeline.

Dependencies

• python 3.x
• python docopt
• minimap2
• bedtools
• seqkit
• r-scales
• r-dplyr
• r-readr
• r-stringr
• r-ggplot2
• r-optparse
• r-tidyr
• r-ggpubr

Create environment nemaChromQC

conda create -y -n nemaChromQC -c conda-forge -c bioconda minimap2 seqkit docopt python=3 bedtools r-scales r-dplyr r-readr r-stringr r-ggplot2 r-optparse r-tidyr r-ggpubr