Caviar (Custom Assemblies via reproducible Pipeline): an open source Nextflow-based pipeline for assembly execution, which includes the tools MEGAHIT, Oases, Trinity, rnaSPAdes, Trans-ABySS, SOAPdenovo-Trans, IDBA-tran and IDBA-MT, largely with default execution parameters.
The pipeline requires executable binaries or scripts in the environment variable. This can be set with
env {
PATH = "/example/path:$PATH"
}
in the nextflow.config file.
Adjust the config file example_resource.config according to your cluster.
Adjust the config file example_params.config with:
sample_dir being the path to the merged fasta samples.
pattern being regex with the paired mate pattern
pattern = "*_R{1,2}.fastq.gz"
and
result_dir = ""
if available: read_length = insert_size =
Caviar requires the binaries fq2fa, idba_tran, idba-mt, velveth, velvetg, oases, rnaspades.py, SOAPdenovo-Trans-127mer, Trinity, megahit binaries in the path.
The process DBG can be commented out in the main.nf.
Miniconda needs to be installed and transabyss in a conda environment named transabyss.
Code sources:
fq2fa, idba_tran
https://github.com/loneknightpy/idba
https://github.com/dzerbino/oases (also clone and build linked velvet version)
https://github.com/voutcn/megahit
https://github.com/ablab/spades
https://github.com/trinityrnaseq/trinityrnaseq
https://bioconda.github.io/recipes/transabyss/README.html
https://github.com/aquaskyline/SOAPdenovo-Trans
https://code.google.com/archive/p/hku-idba-mt/source/default/source