Software Updates

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.

Presto

A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.

MOODS

MOODS is a collection of algorithms used to match position weight matrices (PWM) with DNA sequences.

Bowtie 2

an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

IGV

(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

Severus

Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT).

fibertools-rs

a CLI tool for interacting with fiberseq bam files.

BLAST+

a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.

rasusa

Randomly subsample sequencing reads to a specified coverage.

CellBender

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