Software Updates

GRIDSS

a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.

kalign2

a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.

pbbam

a package that provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.

preseq

a tool aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.

SeqFu

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

slow5tools

a simple toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.

PyEnsembl

a Python interface to Ensembl reference genome metadata such as exons and transcripts. PyEnsembl downloads GTF and FASTA files from the Ensembl FTP server and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files.

AGFusion

a python package for annotating gene fusions from the human or mouse genomes.

AnchorWave

AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals.

gw

a fast browser for genomic sequencing data (.bam/.cram format) used directly from the terminal. GW also allows you to view and annotate variants from vcf/bcf files.

dicey

In-silico PCR and variant primer design

SKA2

SKA2 - Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely related sequences, typically small haploid genomes such as bacteria and viruses.

VSEARCH

an alternative to the USEARCH tool developed by Robert C. Edgar (2010) for which the source code is not publicly available, VSEARCH is an open source, multithreaded 64-bit tool for processing and preparing metagenomics, genomics, and population genomics nucleotide sequence data. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling, and sorting. It also supports FASTQ file analysis, filtering, conversion, and merging of paired-end reads.

RingMapper

a code for performing RING-MaP and PAIR-MaP analysis.

Luna

is an open-source C/C++ software package for manipulating and analyzing polysomnographic recordings, with a focus on the sleep EEG.

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.

MDAnalysis

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

Spyder

is a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.

MDAnalysis

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

R

a free software environment for statistical computing and graphics.

cas-offinder

Cas-OFFinder is OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN).

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.

Segment Anything

(SAM) produces high quality object masks from input prompts such as points or boxes, and it can be used to generate masks for all objects in an image.