BGC2Tree pipeline

For creating phylogenetic trees of homologous proteins from biosynthetic gene clusters

Requirements: (Tested in WSL2 Ubuntu 20.04.2 LTS)

• NextFlow
• Conda

Example local usage:

nextflow run main.nf --in data/example_query.fasta --db data/gbk_records

Remote usage:

nextflow run jbwdn/bgc_2_tree --in your_local_query.fasta --db your_local_direcory_of_gbks

Description:

1. Accept a query fasta containing 1 sequence and a path to a folder containing .gbk records
2. Using phmmer find a potential homolog from each record and save all into a fasta with labels
3. Perform protein sequence alignment using MUSCLE
4. Use alignment to calculate a phylogenetic Tree using FastTree
5. Paths to the three output files (homologs, alignment & tree) printed to stdout

See Nextflow and conda docs for installation instructions.

Built using this template.

References:

• pHMMER: Eddy2009 (10.1142/9781848165632_0019)
• MUSCLE: Edgar2004 (10.1186/1471-2105-5-113)
• FastTree: Price2010 (10.1371/journal.pone.0009490)