Software Updates

Control-FREEC

Copy number and genotype annotation from whole genome and whole exome sequencing data.

TakeABreak

tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes

GSearch

is an ultra-fast and scalable microbial genome search program based on MinHash-like metric and graph-based approximate nearest neighbor search

unikmer

toolkit for k-mer with taxonomic information

medaka

a tool to create consensus sequences and variant calls from nanopore sequencing data.

Metaphor

Metagenomic Pipeline for Short Reads

ChIPs

ChIPs is a tool for simulating ChIP-sequencing experiments.

MetaGraph

The MetaGraph framework allows for indexing and analysis of very large biological sequence collections, producing compressed indexes that can represent several petabases of input data. The indexes can be efficiently queried with any query sequence of interest.

dEploid

deconvolutes mixed genomes with unknown proportions.

GCEN

a command-line toolkit that allows biologists to easily build gene co-expression network and predict gene function, especially in RNA-Seq research or lncRNAs annotation

Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

SRA Toolkit

(Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

shark

Mapping-free filtering of useless RNA-Seq reads

CellProfiler

a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

YaHS

YaHS, yet another Hi-C scaffolding tool

SpydrPick

Mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure

umis

tools for processing UMI RNA-tag data.

CellProfiler

a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

bedtools

a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

LCA

Lowest Common Ancestor calculation tool

fastq-dl

A tool to download FASTQs associated with Study, Experiment, or Run accessions.

TreeTime

provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies.

3D Slicer

is a free and open-source platform for analyzing and understanding medical image data.

Jellyfish

a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.

km

software for RNA-seq investigation using k-mer decomposition