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
• FlexTaxD - https://github.com/FOI-Bioinformatics/flextaxd
• 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 pdf 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

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_export]
                 [--refdir] [--workdir]
                 [--read_input] [--skip_mauve]
                 [--keep_going] [--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_export           no file output (can be used if summary only is requested)
  --summary             Output a summary file and tree with all called SNPs

Run options:
  --refdir              Specify reference directory
  --workdir             Change workdir default (./)
  --read_input          Select if input is reads not fasta
                        (not implemeted expected for version v2.1.0)
  --min_required_hits   MIN_REQUIRED_HITS
                        Minimum sequential hits to call a SNP!
  --keep_going          If Error occurs, continue with the rest of samples
  --rerun               Rerun already processed files (else skip if result file exists)

  --keep_temp           keep temporary files
  --skip_mauve          If xmfa files already exists skip step

Logging and debug options:
  --tmpdir              Specify reference 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.