Installed This software should be available with no extra configuration. samtools-1.16.1 Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
Samtools Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtools Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants HTSlib A C library for reading/writing high-throughput sequencing data Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.
Conda See the ‘activating the conda environment’ section below to access this software. rMATS-turbo-4.1.2
About rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net). The major difference between rMATS turbo and rMATS is speed and space usage. rMATS turbo is 100 times faster and the output file is 1000 times smaller than rMATS. These advantages make analysis and storage of a large scale dataset easy and convenient.
Installed This software should be available with no extra configuration. treemix-1.13 Link to Manual
TreeMix
Authors: JK Pickrell and JK Pritchard
TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.
Installed This software should be available with no extra configuration. ppp-0.1.13 - Popgen Pipeline Platform (PPP) The PPP is a software platform with the goal of reducing the computational expertise required for conducting population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized environment. Functions were developed to encompass entire workflows, including: input preparation, file format conversion, various population genomic analyses, output generation, and visualization.
Conda See the ‘activating the conda environment’ section below to access this software. GTDBtk-2.1.1
GTDB-Tk v2.1.0 was released on May 11, 2022. Upgrading is recommended.
Please note v2.1.0+ is not compatible with GTDB-Tk package R207_v1. It is necessary to upgrade to GTDB-Tk package R207_v2.
GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy (GTDB).
Conda See the ‘activating the conda environment’ section below to access this software.
Bakta: rapid & standardized annotation of bacterial genomes, MAGs & plasmids Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.
