Global core alignment

Tip

This document assume that you have already read through the Usage document

Published global core alignment

As a useful resources for the community, we have published a global core alignemnt, from the NCBI dataset available on NCBI, on this link

Using FASTA sequences

We intend to keep this core alignment updated on a quarterly (or annual ) and are actively looking for funding for long term sustenance.

However, we also want to highlight that it is very straightforward to create custom alignment using the CholeraSeq pipeline.

Essentially, you’d need to

  1. Create a samplesheet with the downloaded/precomputed assemblies (FASTA files) as shown below
sample,fastq_1,fastq_2
AHGB01000000.1,https://github.com/CERI-KRISP/CholeraSeq/raw/b0beafcc6c1315e2782667f0306b10f8b3b7e09a/resources/test_fastas/AHGB01.fasta,
AHGB01000000.2,/path/to/your/fasta/file,
  1. Instruct the pipeline to use the existing global core alignment using the global_core_alignment parameter either on the command or through the parameters yaml file.
Tip

And that’s it! The pipline will automatically process the individual FASTA files as per the existing thresholds and then merge them with the global core alignment.

You can now initiate the pipeline with:

nextflow run https://github.com/CERI-KRISP/CholeraSeq -profile docker -params-file params.yaml

with params.yaml containing:

input: "/path/to/desired/samplesheet.csv"
outdir: "/path/to/desired/output/directory"
global_core_alignment: "/path/to/existing/global_core_alignment"

# other parameters

Using existing local core alignment

In case you have already created a local core alignment (from the initial FASTA assemblies files) and you wish to add it to the global core alignment (or any pre-existing alignment), you can make use of the ``

You can now initiate the pipeline with:

nextflow run https://github.com/CERI-KRISP/CholeraSeq -profile docker -params-file params.yaml

with params.yaml containing:

input: "/path/to/desired/samplesheet.csv"
outdir: "/path/to/desired/output/directory"

# Provide existing core alignments, to be merged
global_core_alignment: "/path/to/existing/global_core_alignment"
cohort_core_alignment : "/path/to/existing/cohort_core_alignment"

# other parameters