Software Updates

mlst

Scan contig files against PubMLST typing schemes

ABRicate

Mass screening of contigs for antibiotic resistance genes

WhatsHap

phase genomic variants using DNA sequencing reads (haplotype assembly)

ARIBA

ARIBA: Antibiotic Resistance Identification By Assembly

peddy

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

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

PHAST

PHAST is a freely available software package for comparative and evolutionary genomics.

fgbio

A set of tools to analyze genomic data with a focus on Next Generation Sequencing

Krona

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

redistributable software libraries to support CUDA applications for Linux.

cd-hit

Clusters and compares protein or nucleotide sequences

CIRCexplorer2

Circular RNA analysis toolkits

SEPP

SATe-enabled phylogenetic placement

prokka

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

TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data

pygtftk

The gtftk suite providing facilities to manipulate genomic annotations in gtf format.

picard-slim

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

HOMER

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

cyvcf2

cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.

phyluce

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.

MUMmer4

MUMmer is a system for rapidly aligning large DNA sequences to one another.

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

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.

kraken2

Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

CrossMap

CrossMap is a program for genome coordinates conversion between different genome assemblies.

R-pkgs-Biogrids

contains common and requested R packages for BIOGRIDS. This title is dependent on R.

Trinotate

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

cellranger-arc

The set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells.

bam-readcount

bam-readcount generates metrics at single nucleotide positions.

circos

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

STREAM

STREAM Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell 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

Barrnap predicts the location of ribosomal RNA genes in genomes. (bacteria, archaea, metazoan mitochondria and eukaryotes.)

MEGAHIT

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph