CanSNPer2

CanSNPer2: A toolkit for SNP-typing NGS data.

Future planned implementations

• Read input - Call SNPs directly from reads instead of an assembly

Databases supplied can be found at https://github.com/FOI-Bioinformatics/CanSNPer2-data

• Francisella tularensis
• Bacillus anthracis
• Yersinia pestis

Upcoming databases

• Brucella
• Coxiella

Installation

Installing using bioconda using mamba (recommended instead of conda)

mamba create -n cansnper2 cansnper2
mamba activate cansnper2

Installing from the repository

python setup.py install

Requirements (for manual install conda will install all dependencies)

• ETE3
• progressiveMauve

Read input (not yet implemeted)

• BWA
• Minimap2

User guide CanSNPer2 (for custom databases see below)

1. Download pre-built databases from https://github.com/FOI-Bioinformatics/CanSNPer2-data

2. Download references for database

CanSNPer2-download --database downloaded_database.db

3. Run genomes

CanSNPer2 --database downloaded_database.db fastadir/*.fasta --summary

The summary parameter will give a final result file with all SNPs that could be confirmed as well as a final CanSNP tree (self-contained html, opens in any browser) with all SNPs from set colored.

For more options CanSNPer2 --help

Quick start custom databases

Create database, download references annotated in the database and run CanSNPer2

CanSNPer2-database --database francisella_tularensis.db --annotation snps.txt --tree tree.txt --reference references.txt --source_type CanSNPer --create
CanSNPer2-download --database francisella_tularensis.db
CanSNPer2 sample1.fasta sample2.fasta --database francisella_tularensis.db --save_tree

CanSNPer2-database

usage: CanSNPer2-database [-h] [-db] [--tree] [--annotation] [--references]
                      [--source_type] [--create] [--mod_file] [--parent]
                      [--remove] [--replace] [--export] [--export_format] [-o]
                      [--tmpdir] [--logs] [--verbose] [--debug] [--supress]

CanSNPer2-database

optional arguments:
  -h, --help         show this help message and exit

Required:
  -db , --database   CanSNPer2 database name

Load database:
  --tree             CanSNPer tree source file
  --annotation       CanSNPer snp source file
  --references       File containing all reference genomes listed
  --source_type      Select source file type
  --create           Create new database!

Database modifications:
  --mod_file         File with modifications/update to the tree
  --parent           Node (or nodes matching tree file) from which to
                     update/replace/remove
  --remove           Remove the whole branch rooted at the --parent node, with
                     its nodes, links and SNP annotations
  --replace          replace node

Export database:
  --export           Export database to text format (exports tree and
                     annotation file)
  --export_format    Select output format [newick, tab]
  -o , --outdir      outdir for database export!

Logging and debug options:
  --tmpdir           Specify tmp directory default (/tmp)
  --logs             Specify log directory
  --verbose          print process info, default no output
  --debug            print debug info
  --supress          supress warnings

CanSNPer2-download

usage: CanSNPer2-download [-h] -db  [-s] [-o] [--logs] [--verbose]

CanSNPer2-download

optional arguments:
  -h, --help         show this help message and exit

Required:
  -db , --database   CanSNP database

Download options:
  -s , --source      Source for download (genbank/refseq)
  -o , --outdir      reference genomes folder

Logging and debug options:
  --logs             Specify log directory
  --verbose          Verbose logging

Example structure of references.txt

genome strain  genbank_id      refseq_id       assembly_name
OSU18   OSU18   GCA_000014605.1 GCF_000014605.1 ASM1460v1
FSC200  FSC200  GCA_000168775.2 GCF_000168775.2 ASM16877v2
FTNF002-00      FTNF002-00      GCA_000017785.1 GCF_000017785.1 ASM1778v1
LVS     LVS     GCA_000009245.1 GCF_000009245.1 ASM924v1
SCHUS4.2        SCHUS4  GCA_000008985.1 GCF_000008985.1 ASM898v1

Example structure of snps.txt (NEW headerline)

snp_id	strain	reference	genome	position	derived_base	ancestral_base
T/N.1	francisella	Svensson2009	SCHUS4.2	83976	A	G
T.1	francisella	Svensson2009	SCHUS4.2	1165688	G	A
M.1	francisella	Vogler2009	SCHUS4.2	75124	T	C
A/M.1	francisella	Vogler2009	SCHUS4.2	1491914	A	G
A.1	francisella	Vogler2009	SCHUS4.2	397639	T	C
B.1	francisella	Birdsell2014	OSU18	1710718	T	C
...

Example structure of tree.txt

T/N.1
T/N.1	T.1		
T/N.1	T.1	B.1
T/N.1	T.1	A/M.1
T/N.1	T.1	A/M.1	A.1
T/N.1	T.1	A/M.1	M.1
...

CanSNPer2 help

usage: CanSNPer2 [-h] [-db] [-o DIR] [--save_tree] [--no_snpfiles]
               [--summary] [--refdir] [--workdir] [--read_input]
               [--min_required_hits MIN_REQUIRED_HITS]
               [--strictness STRICTNESS] [--mask MASK] [--keep_going]
               [--rerun] [--skip_mauve] [--keep_temp] [--tmpdir]
               [--logdir] [--verbose] [--debug] [--supress]
               [query [query ...]]

CanSNPer2

optional arguments:
  -h, --help            show this help message and exit

Required arguments:
  query                 File(s) to align (fasta)
  -db , --database      CanSNP database

Output options:
  -o DIR, --outdir DIR  Output directory
  --save_tree           Save tree as PDF using ETE3 (default False)
  --no_snpfiles         Don´t save output files.
  --summary             Output a summary file and tree with all called SNPs
                        not affected by no_snpfiles

Run options:
  --refdir              Specify reference directory
  --workdir             Change workdir default (./)
  --read_input          Select if input is reads not fasta
  --min_required_hits MIN_REQUIRED_HITS
                        Minimum sequential hits to call a SNP!
  --strictness STRICTNESS
                        Fraction of the SNPs on the path to the final SNP
                        that must be called; SNPs without alignment data count
                        against it, an ancestral SNP stops the path (0-1,
                        default 0.7)
  --mask MASK           Ignore SNPs closer than this many bases to the edge of
                        an alignment (default 0, off)
  --keep_going          If Error occurs, continue with the rest of samples
  --rerun               Rerun already processed files (else skip if result
                        file exists)
  --skip_mauve          If xmfa files already exists skip step
  --keep_temp           keep temporary files

Logging and debug options:
  --tmpdir              Specify tmp directory default (/tmp/CanSNPer2)

Each run that aligns writes its temporary files to its own directory,
`<tmpdir>/CanSNPer2/run_<random>`, and removes only that directory when it
finishes, so several runs can share the same `--tmpdir`. With `--keep_temp` the
directory is kept and its path is logged; the alignments in it can be reused
with `--skip_mauve --tmpdir <that directory>`.
  --logdir              Specify log directory
  --verbose             Verbose output
  --debug               Debug output
  --supress             Supress warnings

Additional information about running CanSNPer2 could be found in the wiki.

About this software

Copyright (C) 2019 David Sundell @ FOI bioinformatics group

CanSNPer2 is implemented as a Python 3 package. It is open source software made available under the GPL-3.0 license.

If you experience any difficulties with this software, or you have suggestions, or want to contribute directly, you have the following options:

• submit a bug report or feature request to the issue tracker
• contribute directly to the source code through the github repository. 'Pull requests' are especially welcome.