kfwins2022/gaap-bp

Genome Assembly and Annotation Pipeline for Bacteria Pacbio

GAAP-BP

GAAP-BP v. 1.0 - Genome Assembly and Annotation Pipeline for Bacteria Pacbio

MIT LICENSE - Copyright © 2022 Gian M.N. Benucci, Ph.D.
email: benucci[at]msu[dot]edu
Gisa-BP v.1, October 2022

This pipeline is based upon work supported by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award DE-SC0018409

Installation

To use Gisa-PB just clone the directory

git clone [email protected]:Gian77/GAAP-BP.git

You will then need to

• Copy your raw reads file in the rawdata directory together with a md5sum file.
• Install all the necessary tools through conda (please see the complete list of tools reported below).
• Download the databases (please see below and the config.yaml file), and include the full paths into the config file.
• Select all the User options (please see below).

Then you should be good to go and run Gisa-PB by just sh Gisa-PB-v1.sh

Let's explore the settings in the config.yaml file

Directories

The main project's directory is: project_dir="/mnt/home/benucci/genome-pipe-bac-pb. Of course, you will need to adjust the path to your HPCC user name.

IMPORTANT NOTEs

• This pipeline was born for running on the HPCC at Michigan State University on the dev-amd20 (which as 128 cpus per node). If you want to run this piepline in any other systems it will require (possibly substantial) modification of the main, as well as, the accessory scripts.
• You can change the name of the project directory. However, you will not be able to change the other direcotiry names (i.e. outputs and slurms) becasue they are part of the workflow, unless you want to modify the individual scripts.
• Please check the config file for options. A few script are additional and are can be avoided to save time.

Default to the rawdata directory

When the config is sourced it defaults to the rawdata project directory

cd $project_dir/rawdata/

Databases

Find a place in your lab space (or in your home directory) where to put all the needed databases. Correct the directory hierarchy according to your HPCC account name.

NCBI_nt="/mnt/research/ShadeLab/Benucci/databases/ncbi_nt1121"
kraken2_db="/mnt/research/ShadeLab/Benucci/databases/kraken2_db/"
minikraken2_db="/mnt/research/ShadeLab/Benucci/databases/minikraken2_db/"
dmnd_bac="/mnt/research/ShadeLab/Benucci/databases/emapperdb/eggdb_bacteria.dmnd"
platon_db="/mnt/research/ShadeLab/Benucci/databases/platon_db/db/"
mash_plsdb="/mnt/research/ShadeLab/Benucci/databases/plasmid_db/plsdb.msh"
mash_plsdb_meta="/mnt/research/ShadeLab/Benucci/databases/plasmid_db/plsdb.tsv"
busco_db="/mnt/research/ShadeLab/Benucci/databases/busco_db1121/bacteria_odb10"

PATHs

export GTDBTK_DATA_PATH=/mnt/research/ShadeLab/Benucci/databases/gtdb_tk/release207_v2
export EGGNOG_DATA_DIR=/mnt/research/ShadeLab/Benucci/databases/emapperdb/
export GUNC_DB=/mnt/research/ShadeLab/Benucci/databases/gunc_db/gunc_db_progenomes2.1.dmnd

User options

If not numeric (i.e. float) then yes or no.

MASH=yes
BAKTA=no
EGGNOG=yes
CHROMOSOMES=5

Software needed to fully run Gisa-PB on HPCC

Please install via conda (or use the binaries in the HPPC) of all these software below.

• FastQC

• NanoStat

• Flye

• Minimap2

• Racon

• Pilon

• Circlator

• quast

• qualimap

• BLAST

• BlobTools

• Platon

• Mash

• Kraken 2

• Bracken

• CheckM

• GTDB-Tk

• Barrnap

• Metaxa2

• eggNOG

• Prokka

• Bakta

• BUSCO

• ABRicate

• MultiQC

• Bandage