CanSNPer2: A toolkit for SNP-typing.

CanSNPer2: A toolkit for SNP-typing.
Copyright (C) 2019 David Sundell @ FOI bioinformatics group

The second release of CanSNPer (CanSNPer2) is exclusively written for python3
CanSNPer2 is simplified from CanSNPer1 stripped to only perform
required tasks. It is also written in a modular form with separate
classes for each task which allows future extentions such as a sequence read
input option planned during 2020.

Requires:

progressiveMauve
FlexTaxD >= v0.2.1
ETE3

VERSION 2.0.6

[New]

• --strictness parameter added: Default 70% (0.7) of SNPs in a path must be valid for a call, this can be adjusted by setting strictness. However if a ancestral SNP is found in the path it will be invalid.
• --summary option added: Add a summary file and a tree with all unique SNPS from a set of result files (_snps.txt)
• requires FlexTaxD v0.2.1 or later

CanSNPer2: A toolkit for SNP-typing

CanSNPer2: A toolkit for SNP-typing.
Copyright (C) 2019 David Sundell @ FOI bioinformatics group

The second release of CanSNPer (CanSNPer2) is exclusively written for python3
CanSNPer2 is simplified from CanSNPer1 stripped to only perform
required tasks. It is also written in a modular form with separate
classes for each task which allows future extentions such as a sequence read
input option planned during 2020.

Requires:

progressiveMauve
FlexTaxD >= v0.2.0
ETE3

VERSION 2.0.3

[New]

• A self installation test has been added due to problems of verifying the ete3 installation during conda packaging.

CanSNPer2: A toolkit for SNP-typing

CanSNPer2: A toolkit for SNP-typing.
Copyright (C) 2019 David Sundell @ FOI bioinformatics group

The second release of CanSNPer (CanSNPer2) is exclusively written for python3
CanSNPer2 is simplified from CanSNPer1 stripped to only perform
required tasks. It is also written in a modular form with separate
classes for each task which allows future extentions such as a sequence read
input option planned during 2020.

Requires:

• progressiveMauve
• FlexTaxD >= v0.2.0
• ETE3

VERSION 2.0.2

[New]

• CanSNPer2 will now output [name of genome:\tSNPname] (or NA if not called) to termina by default, --supress can be used to avoid other outputs including warnings (not errors).

• --keep_going can be used when processing a large number of genomes to force the program to continue with the next genome instead of stopping if an error occurs.

• CanSNPer2-download will automatically download genomes annotated in the CanSNPer2 database to a directory for use during SNPcalling

• Custom databases can be created using CanSNPer2-database

• Pre-built databases and sources can be found at https://github.com/FOI-Bioinformatics/CanSNPer2-data
  Observe that references needs to be downloaded also for pre-built databases using CanSNPer2-download!

CanSNPer2: A toolkit for SNP-typing NGS data

CanSNPer2: A toolkit for SNP-typing NGS data.
Copyright (C) 2019 David Sundell @ FOI bioinformatics group

VERSION 2.0.1 First release of CanSNPer2

The second release of CanSNPer (CanSNPer2) is exclusively written for python3
CanSNPer2 is simplified from CanSNPer1 stripped to only perform
required tasks. It is also written in a modular form with separate
classes for each task which allows future extentions such as a sequence read
input option planned during 2020.

Requires
progressiveMauve
FlexTaxD >= v0.2.0
ETE3