Virus assembly module used by viridian
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.
These must be installed and in your $PATH:
racon(https://github.com/lbcb-sci/racon)minimap2(https://github.com/lh3/minimap2/).
Clone this repository and run:
python3 -m pip install .
Clone this repository and run:
sudo singularity build cylon.img Singularity.def
to build the container cylon.img.
Required input:
- Reference FASTA file
- JSON file of amplicons. Described below. end end positions of the amplicons
- 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
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.