Software Updates

VCFtools

a program package designed to provide easily accessible methods for working with complex genetic variation data in the form of VCF files, such as those generated by the 1000 Genomes Project.

antiSMASH

antiSMASH (antibiotics and Secondary Metabolite Analysis SHell) allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.

Cell Ranger

a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.

BISCUIT

BISulfite-seq CUI Toolkit (BISCUIT) is a utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data. It was written to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data.

SVDSS

SVDSS is a method for structural variations discovery from accurate long reads (e.g PacBio HiFi), based on the notion of sample-specific strings (SFS, or simply specific strings).

BioPhi

BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.

BWA

(Burrows-Wheeler Aligner) a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.

pyPINTS

Explore distal transcriptional regulatory elements (TREs) identified from nascent-transcript sequencing.

nextclade

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

Flye

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

nextclade

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

Flye

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

CapCruncher

is designed to process Capture-C, Tri-C and Tiled-C data. Unlike other pipelines that are designed to process Hi-C or Capture-HiC data, the filtering steps in CapCruncher are specifically optimized for these datasets.

oarfish

is a program for quantifying transcript-level expression from long-read (i.e. Oxford nanopore cDNA and direct RNA and PacBio) sequencing technologies.

AlphaFold

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

R

a free software environment for statistical computing and graphics.

PyTorch

an open source deep learning platform that provides a seamless path from research prototyping to production deployment.