Software Updates

Stacks

a software pipeline for building loci from RAD-seq.

Scalpel

a software package for detecting INDELs.

OrthoFinder

a fast, accurate and comprehensive platform for comparative genomics, OrthoFinder is accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy!

tRNAscan-SE

tRNA detection in large-scale genome sequence.

Kaiju

fast and sensitive taxonomic classification for metagenomics.

AUGUSTUS

a gene prediction program for eukaryotes that can be used as an ab initio program, which means it bases its prediction purely on the sequence.

Minimap2

is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments.

RAxML

(Randomized Axelerated Maximum Likelihood) a tool for phylogenetic analysis and post-analysis of large phylogenies.

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

CellBender

a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

R

a free software environment for statistical computing and graphics.

atropos

trim adapters from high-throughput sequencing reads.

Flye

fast and accurate de novo assembler for single molecule sequencing reads.

Bakta

rapid and standardized annotation of bacterial genomes & plasmids.

metagenome-atlas

ATLAS - Three commands to start analysing your metagenome data

AGAT

(Another Gff Analysis Toolkit) a suite of tools to handle gene annotations in any GTF/GFF format.

mOTUs

marker gene-based OTU (mOTU) profiling.

GimmeMotifs

a suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments.

Mykrobe

antibiotic resistance prediction in minutes.

Raven

a de novo genome assembler for long uncorrected reads.

seqMINER

an integrated ChIP-seq data interpretation platform.

Fiji

an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

snp-dists

converts a FASTA alignment to SNP distance matrix.

MUMmer

a versatile alignment tool for DNA and protein sequences.

SRA Toolkit

(Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

vcflib

command-line tools for manipulating VCF files.

sourmash

quickly searches, compares, and analyzes genomic and metagenomic data sets.

LAST

finds & aligns related regions of sequences. LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes).

Peakhood

a tool that takes a set of CLIP-seq peak regions and for each region, individually extracts the most likely site context (transcript or genomic).

SWORD

(Smith Waterman On Reduced Database) is a fast and sensitive software for protein sequence alignment.

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

Platypus

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme.

STAR

(Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.

QuickTree

an efficient implementation of the Neighbor-Joining algorithm.

CellProfiler

a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.