BugBuilder NRW
Updates to the BugBuilder pipeline incorporating two major chanages:
- Ability to submit --trusted-contigs to SPAdes
- Ability to restart an analaysis after the (timeconsuming) assembly step
Additionally, various bug fixes were incorportated to make it work with more recent versions of some of the programs.
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Hands-free microbial genome assembly
BugBuilder is a pipeline to facilitate assembly and annotation of database submission-ready, draft-quality microbial genomes from high-throughput sequencing data. It utilises a range of existing tools to produce an annotated genome assembly (optionally scaffolded against a reference genome), outputting EMBL formatted records describing the assembled contigs, and AGP v2 files describing the scaffolds. Required inputs are fastq format reads from either a fragmment of paired-end sequencing run, and optionally a reference genome sequence in fasta format.
BugBuilder is implemented in Perl and is distributed under the Artistic License v2.0
Everything is now available to install via conda:
conda create --name bugbuilder abyss amos aragorn arrow barrnap biopython blast bwa cgview curl fastqc gmp gnuplot minced mummer mkl parallel pilon prokka picard prodigal pyyaml samtools sis seqtk sickle-trim spades tabulate tbl2asn hmmer vcflib
source activate bugbuilder
then, clone this repo, and install:
python setup.py install
To set the configuration, run the following command:
BugBuilder --configure
and you are ready to go! Have a try with the test data first:
BugBuilder --platform illumina -o output --assemblers spades --fastq1 ./tests/references/2chrom1.fq --fastq2 ./tests/references/2chrom2.fq --reference ./tests/references/2chrom.fasta --scaffolder sis --finisher pilon
A virtual machine image preconfigured with the freely redistributable prerequistite packages is available from http://web.bioinformatics.ic.ac.uk/BugBuilder/BugBuilder_current.vdi
The latest version of the software can be downloaded by running:
git clone git://github.com/jamesabbott/BugBuilder/
Full installation and configuration instructions are available in the user guide, which can be obtained from http://www.imperial.ac.uk/bioinformatics-support-service/resources/software/BugBuilder/, or if you have latex installed on your machine you can build the documentation locally:
[jamesa@codon ~]$ cd BugBuilder/doc
[jamesa@codon ~]$ ./build.sh
conda create -n bug python==3.5 spades==3.9 fastqc sickle-trim