Software Updates

demuxlet

Genetic multiplexing of barcoded single cell RNA-seq.

Cutadapt

finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

UPIMAPI

(UniProt Id Mapping through API) a command line interface for using UniProt's API, which allows access to UniProt's ID mapping programmatically.

clustalo

is the latest version of Clustal: a multiple sequence alignment program for DNA or proteins.

BEAGLE

is a software package for phasing genotypes and imputing ungenotyped markers.

Nextalign

Viral genome sequence alignment tool

nextclade

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

mega2

(Manipulation Environment for Genetic Analyses) - data-handling program for facilitating genetic linkage and association analyses.

pbsv

PacBio structural variant (SV) calling and analysis tools

lima

is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data.

shorah

Short Reads Assembly into Haplotypes (ShoRAH) program for inferring viral haplotypes from NGS data

sourmash

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

mentalist

MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance.

ivar

is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

Entrez Edirect Utilities

provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

htstream

is a quality control and processing pipeline for High Throughput Sequencing data.

bcalm

is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.

ColabFold

an easy-to-use Notebook based environment for fast and convenient protein structure predictions.

umap-learn

(UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction

MultiQC

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

hatchet

(Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

HiCExplorer

is a set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data.