Software Updates

AlphaFold

an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.

MMseqs2

an ultra fast and sensitive sequence search and clustering suite

abeona

a simple transcriptome assembler based on kallisto and Cortex graphs.

Proteinortho

a tool to detect orthologous genes within different species.

RTG Tools

(RealTimeGenomics Tools) utilities for accurate VCF comparison and manipulation.

mlst

scan contig files against PubMLST typing schemes.

ABRicate

mass screening of contigs for antibiotic resistance genes.

WhatsHap

a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.

ARIBA

(Antibiotic Resistance Identification By Assembly) a tool that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

peddy

compares familial-relationships and sexes as reported in a PED/FAM file with those inferred from a VCF.

IntaRNA

efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites.

HMMER

is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

Cactus

a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs.

PHAST

(Phylogenetic Analysis with Space/Time models) a software package for comparative and evolutionary genomics.

Krona Tools

is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

umis

tools for processing UMI RNA-tag data.

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.

cd-hit

clusters and compares protein or nucleotide sequences.

CIRCexplorer2

a comprehensive and integrative circular RNA analysis toolset.

SEPP

(SATe-enabled Phylogenetic Placement) addresses the problem of phylogenetic placement of short reads into reference alignments and trees.

Prokka

a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.

pygtftk

(Python GTF toolkit) a suite providing facilities to manipulate genomic annotations in gtf format.

HOMER

(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.

cyvcf2

a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.

phyluce

(phy-loo-chee) is a software package that is useful for analyzing both data collected from UCE loci and also data collection from other types of loci for phylogenomic studies at the species, population, and individual levels.

andi

estimates the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

Bracken

(Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Kraken 2

a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

CrossMap

a program for genome coordinates conversion between different genome assemblies.

Trinotate

a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

bam-readcount

bam-readcount generates metrics at single nucleotide positions.

Circos

a software package for visualizing data and information. It visualizes data in a circular layout.

STREAM

(Single-cell Trajectories Reconstruction, Exploration And Mapping) is an interactive computational pipeline for reconstructing complex celluar developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data.

swarm

a robust and fast clustering method for amplicon-based studies.

MultiQC

aggregates results from bioinformatics analyses across many samples into a single report.

Racon

ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.

Barrnap

(BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes (bacteria, archaea, metazoan mitochondria and eukaryotes).

MEGAHIT

an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.