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cylon

Virus assembly module used by viridian

Important

We recommend that you use Viridian instead of this repository. This repository is intended to be run by Viridian, not to be used as a stand-alone tool. Viridian provides a complete end-to-end pipeline for generating a consensus sequence from reads.

Install

From source

These must be installed and in your $PATH:

Clone this repository and run:

python3 -m pip install .

Singularity container

Clone this repository and run:

sudo singularity build cylon.img Singularity.def

to build the container cylon.img.

Example usage

Required input:

  1. Reference FASTA file
  2. JSON file of amplicons. Described below. end end positions of the amplicons
  3. Reads, either in a sorted mapped indexed BAM file, or in a FASTA/FASTQ file (or two FASTA/FASTQ files for paired reads).

The amplicons JSON file must look like this:

{
  "amplicon1": {
    "start": 10,
    "end": 399,
    "left_primer_end": 30,
    "right_primer_start": 390
  },
  "amplicon2": { ... etc ...}
}

The keys are the amplicon names, and the values are the details for each amplicon. All coordinates are 0-based inclusive. The start and end entries are the positions of the start and end of the amplicon. left_primer_end is the rightmost position of the end of the left primer, and right_primer_start is the leftmost position of the right primer. This means for each amplicon we should have: start < left_primer_end < right_primer_start < end. (Other key/values can be inside the dictionary for each amplicon, but will simply be ignored).

Run using a mapped BAM file of ONT reads:

cylon assemble --bam reads.bam ont ref.fasta amplicons.json outdir

Run using a FASTQ file of ONT reads:

cylon assemble --reads_to_map reads.fastq ont ref.fasta amplicons.json outdir

Run using two FASTQ files of paired Illumina reads:

cylon assemble \
  --reads_to_map reads1.fastq --mates_to_map reads2.fastq \
  illumina ref.fasta amplicons.json outdir

Output

The important files are:

  • consensus.final_assembly.fa: this contains the consensus sequence.
  • amplicon_data.json: JSON file containing details of what happened when trying to make a consensus sequence of each amplicon.