sphaehost

Bacterial asembly and annotation

This is an extension of sphae (https://github.com/linsalrob/sphae). Sphae assembled and annotates phage genomes, here I am assembling and annotating the bacterial hosts.

Install

Steps for installing sphae workflow

#clone sphae repository
git clone https://github.com/npbhavya/sphaehost.git

#move to sphae folder
cd sphaehost

#install sphae
pip install -e .

#confirm the workflow is installed by running the below command 
sphaehost --help

Installing databases

Run command,

sphaehost install

Running the workflow

The command sphaehost run will run QC, assembly and annotation

Commands to run

Only one command needs to be submitted to run all the above steps: QC, assembly and assembly stats

#For illumina reads, place the reads both forward and reverse reads to one directory
sphaehost run --input sample-data/illumina --output example -k 

#For nanopore reads, place the reads, one file per sample in a directory
sphaehost run --input sample-data/nanopore --sequencing longread --output example -k

#To run either of the commands on the cluster, add --profile slurm to the command. For instance here is the command for longreads/nanopore reads 
#Before running this below command, make sure have slurm config files setup, here is a tutorial, https://fame.flinders.edu.au/blog/2021/08/02/snakemake-profiles-updated 
sphaehost run --input sample-data/illumina --preprocess longread --output example --profile slurm -k

Output

Need to generate the results folder