ProkaryoteAssembly

Two simple scripts to assemble prokaryotic genomes using paired-end reads.

Pipeline Overview

1. QC on reads with bbduk.sh (adapter trimming/quality filtering)
2. Error-correction of reads with tadpole.sh
3. Assembly of reads with skesa
4. Alignment of error-corrected reads against draft assembly with bbmap.sh
5. Polishing of assembly with pilon

Installation

pip install ProkaryoteAssembly

Usage

The first script, prokaryote_assemble.py, operates on a single sample at a time.

Usage: prokaryote_assemble.py [OPTIONS]

Options:
  -1, --fwd_reads PATH  Path to forward reads (R1) (gzipped FASTQ).
                        [required]
  -2, --rev_reads PATH  Path to reverse reads (R2) (gzipped FASTQ).
                        [required]
  -o, --out_dir PATH    Root directory to store all output files.  [required]
  -m, --memory TEXT     Amount of memory to allocate to job. e.g. "8g".
                        Defaults to 8g.
  --cleanup             Specify this flag to delete all intermediary files
                        except the resulting FASTA assembly.
  --version             Specify this flag to print the version and exit.
  --help                Show this message and exit.

The second script, prokaryote_assemble_dir.py, will detect all *.fastq.gz files in a directory and run the assembly pipeline on each sample it can pair.

Usage: prokaryote_assemble_dir.py [OPTIONS]

Options:
  -i, --input_dir PATH  Directory containing all *.fastq.gz files to
                        assemble.NOTE: Files must be gzipped in order to be
                        detected.  [required]
  -o, --out_dir PATH    Root directory to store all output files.  [required]
  -f, --fwd_id TEXT     Pattern to detect forward reads. Defaults to "_R1".
  -r, --rev_id TEXT     Pattern to detect reverse reads. Defaults to "_R2".
  -m, --memory TEXT     Memory to allocate to pilon call. Defaults to 8g (i.e.
                        pilon -Xmx8g). May need to provide a large amount of
                        memory for large read sets/assemblies.
  --cleanup             Specify this flag to delete all intermediary files
                        except the resulting FASTA assembly.
  --version             Specify this flag to print the version and exit.
  --help                Show this message and exit.

Python (3.6) Dependencies

• click

External Dependencies

NOTE: All external dependencies must be available via PATH.

Versions confirmed to work are in brackets.

• skesa (SKESA v.2.1-SVN_551987:557549M)
• BBMap (BBMap version 38.22)
• samtools (samtools 1.8 using htslib 1.8)
• pilon (Pilon version 1.22)

Note: Strongly recommend installing pilon via conda e.g. https://bioconda.github.io/recipes/pilon/README.html

conda install pilon