B-assembler is a snakemake-based pipeline for assembling bacterial genomes from long reads (nanopore or pacbio) or hybrid reads (long and short reads)

Introduction

As input, B-assembler takes one of the following:

• A set of long reads (Nanopore or pacbio) from a bacterial isolate (uncorrected long reads are fine, though corrected long reads should work too)
• Illumina reads from a bacterial isolate (required paired-end reads) and long reads from the same isolate (best case)

Reasons to use B-assembler:

• It is a best-practice for long reads bioinformatics into a (hopefully) easy-to-use pipeline, taking advantage of all the goodness of Snakemake while adding a few features; including:
  • a text-based read config that allows automated simple read pre-processing (select reads based on read length)
  • a text-based run config that provides a trivial way to define assembly and polishing strategies (long read only or hybrid read mode)
  • automatic generation of assembly
• It circularises genome without the need for a separate tool like Circlator.
• It can use long reads or hybrid reads in hybrid assembly.
• It has very low misassembly rates.
• It's easy to use: runs with just one command and usually doesn't require tinkering with parameters.
• It is fast. Running time just need few hours.

Reasons to not use B-assembler:

• You're assembling a eukaryotic genome or a metagenome (Pipeline is designed exclusively for bacterial isolates).
• Your long reads are low depth (<50).
• Your Illumina reads and long reads are from different isolates.
• only Illumina reads.

Requirements

• Linux or macOS
• B-assembler base on conda, the environments include snakemake are installed by conda, conda:https://conda.io/projects/conda/en/latest/user-guide/install/linux.html
• Python 3.6 or later
• Environments of conda installed tools
  • Flye v2.7 (https://github.com/fenderglass/Flye)
  • Racon (https://github.com/isovic/racon)
  • BWA mem (https://sourceforge.net/projects/bio-bwa/files/)
  • Pilon (pilon1.23.jar) (https://github.com/broadinstitute/pilon)
  • Samtools v1.0 or later (https://sourceforge.net/projects/samtools/files/samtools/)
  • Minimap2 v2.1 (https://github.com/lh3/minimap2)
  • blast (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)

Installation

Install from source

git clone https://github.com/huang1990/B-assembler.git; cd B-assembler;

setup the environment

conda env create -n B-assembler -f env.yaml
conda activate B-assembler

Note It is important that you ensure all bioconda installed tools installed.

Write your configuation

###Provide sequence data in config.yaml file

vi config.yaml

Replace the YAML keys as appropriate. Keys are:

Key	Type	Description
longread	Path to Nanopore or Pacbio reads	It requires path to your long reads, pull all your reads into one fastq file, it is recommended to provide absolute path, you can ignore this if you do not have nanopore reads
Illumina R1	path to Illumina R1	Read1 of paired-end Illumina reads, it is recommended to provide absolute path, you can ignore this if you do not have Illumina reads
Illumina R2	path to Illumina R2	Read2 of paired-end Illumina reads, it is recommended to provide absolute path, you can ignore this if you do not have Illumina reads
genomesize	int	number of base pair of extimated genomesize of your species
readtype	ONT or pb	Type of your long reads, ONT is for nanopore, pb is for pacbio

Engage the pipeline

Run the pipeline, you must specify cores to ensure that how many threads you give. ##Usage

Usage: bash run_B-assembler.sh <numCPUs> <LongReadOnly|Hybrid> [output:PWD]

Require arguments:
numCPUs: int
         threads provided for pipeline

LongReadOnly|Hybrid
         assembly mode for your reads, type "LongReadOnly" or "Hybrid" based on your data

Optional argument:
output:
	 output directory, current working directory by default

##Examples

bash run_B-assembler.sh 2 LongReadOnly

output

The final assembly will be in the output directory, and the name of assembly: B-assembler.fasta