Software Updates

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

TensorFlow

an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning, and the flexible numerical computation core is used across many other scientific domains.

SECAPR

Process sequence-capture FASTQ files into alignments for phylogenetic analyses. Integrates allele phasing.

chewBBACA

A complete suite for gene-by-gene schema creation and strain identification.

NanoSim

NanoSim is a fast and scalable read simulator for Nanopore sequencing data.

MOB-suite

MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.

EggNOG-mapper

Fast genome-wide functional annotation through orthology assignment.

AMPtk

AMPtk: Amplicon tool kit for processing high throughput amplicon sequencing data.

Raven

a de novo genome assembler for long uncorrected reads.

ToulligQC

A post sequencing QC tool for Oxford Nanopore sequencers

FsnViz

Tool for plotting gene fusion events detected by various tools using Circos.

GMAP

Genomic mapping and alignment program for mRNA and EST sequences.

HiCUP

A tool for mapping and performing quality control on Hi-C data

nextclade

SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks

Nextalign

Viral genome sequence alignment tool

nanoq

Ultra-fast quality control and summary reports for nanopore reads

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases