Software Updates

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

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

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

CapCruncher

The CapCruncher package 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

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.