hifibgc 0.1.7

Detect Biosynthetic Gene Clusters (BGCs) in HiFi metagenomic data

HiFiBGC

Detect Biosynthetic Gene Clusters (BGCs) in HiFi metagenomic data.

Installation

Conda

conda create -n hifibgc -c conda-forge -c bioconda -c amityadav -y hifibgc
conda activate hifibgc

Usage

Install

hifibgc install

Above command need to be run only once. It installs a required database and a tool.

Test

hifibgc test

Checks hifibgc on a small test data. On completion of above command, you should see something like Snakemake finished successfully on terminal and an output directory hifibgc1.out.

Run

Run hifibgc with defaults:
hifibgc run --input input.fastq # --input is required

Specify output directory and no of threads:
hifibgc run --input input.fastq --output outdir --threads 16

Specify bigscape_cutoff option:
hifibgc run --input input.fastq --bigscape_cutoff 0.4

Output

05_final_output/ 
    BGC_all_metadata.tsv  -->  summary file containing metadata for all BGCs 
    BGC_representative/ -->  directory containing representative BGCs (.gbk files) 
    BGC_all/ -->  directory containing all BGCs (.gbk files) 
    upsetplot_0.3.[pdf|jpg] -->  upsetplot comparing three assemblers (hifiasm-meta, metaflye and hicanu), and unmapped reads