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CanSNPer2: A toolkit for SNP-typing

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@davve2 davve2 released this 16 Apr 06:45
· 19 commits to master since this release
v2.0.2
ff2e288

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!

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