Software Updates

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.

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.

NGMLR

(coNvex Gap-cost alignMents for Long Reads) a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

NGMLR

(coNvex Gap-cost alignMents for Long Reads) a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes.

MetaEuk

a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.

PLASS

(Protein-Level ASSembler) a software to assemble short read sequencing data on a protein level.

SpacePHARER

(CRISPR Spacer Phage-Host pAiRs findER) a modular toolkit for sensitive phage-host interaction identification using CRISPR spacers.

spaTyper

computational method for finding spa types.

pangolin

(Phylogenetic Assignment of Named Global Outbreak LINeages) software package for assigning SARS-CoV-2 genome sequences to global lineages.

UShER

a program that rapidly places new samples onto an existing phylogeny using maximum parsimony. It is particularly helpful in understanding the relationships of newly sequenced SARS-CoV-2 genomes with each other and with previously sequenced genomes in a global phylogeny.

varlociraptor

flexible, arbitrary-scenario, uncertainty-aware variant calling with parameter free filtration via FDR control.

smallgenomeutilities

a collection of scripts that is useful for dealing and manipulating NGS data of small viral genomes.

TOBIAS

(Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal) a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data.

TreeSAPP

a functional and taxonomic annotation tool for microbial genomes and proteins.

StringTie

a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads. In order to identify differentially expressed genes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).

SPAdes

(St. Petersburg genome assembler) a genome assembly algorithm designed for single-cell and multi-cell bacterial data sets.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

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.

Genrich

a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).

fastv

an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data.

WiggleTools

The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank sum test, etc).

GNUVID

(GNU-based Virus IDentification) a Python3 program for Gene Novelty Unit-based Virus Identification for SARS-CoV-2. It ranks CDS nucleotide sequences in a genome fna file based on the number of observed exact CDS nucleotide matches in a public or private database. It was created to type SARS-CoV-2 genomes using a whole genome multilocus sequence typing (wgMLST) approach.

RNAblueprint

The RNAblueprint library solves the problem of stochastically sampling RNA/DNA sequences compatible to multiple structural constraints.

Raven

a de novo genome assembler for long uncorrected reads.

LongGF

a computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing

Ultraplex

an all-in-one software package for processing and demultiplexing fastq files.

bioinfokit

The bioinfokit toolkit aims to provide various easy-to-use functionalities to analyze, visualize, and interpret the biological data generated from genome-scale omics experiments.

EMu

EMu is a relative abundance estimator for 16S genomic sequences

NanoStat

calculates various statistics from a long read sequencing dataset in fastq, bam or albacore sequencing summary format.

refgenie

(reference genome manager) manages storage, access, and transfer of reference genome resources.

Nanopolish

software package for signal-level analysis of Oxford Nanopore sequencing data.

DIAMOND

a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.

VIRULIGN

a tool for codon-correct pairwise alignments, with an augmented functionality to annotate the alignment according the positions of the proteins.

HiLine

HiC alignment and classification pipeline.

BioHansel

subtype microbial whole-genome sequencing (WGS) data using SNV targeting k-mer subtyping schemes.

RODEO

(Rapid ORF Description & Evaluation Online) evaluates one or many genes, characterizing a gene neighborhood based on the presence of profile hidden Markov models (pHMMs).

Rust-Bio-Tools

a set of ultra fast and robust command line utilities for bioinformatics tasks based on Rust-Bio.

ont_fast5_api

is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format.

SECIMTools

a suite of tools for processing of metabolomics data.

MetaGraph

The MetaGraph framework allows for indexing and analysis of very large biological sequence collections, producing compressed indexes that can represent several petabases of input data. The indexes can be efficiently queried with any query sequence of interest.

mokapot

fast and flexible semi-supervised learning for peptide detection.

msstitch

a tool to integrate a number of Shotgun proteomics tools, generating ready to use result files.

dRep

a python program for rapidly comparing large numbers of genomes, dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.

NGMLR

(coNvex Gap-cost alignMents for Long Reads) a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes.

PLINK

a comprehensive update to Shaun Purcell's PLINK command-line program -- a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses.

SeqFu

(Sequece Fastx Utilities) a general-purpose program to manipulate and parse information from FASTA/FASTQ files.