Software Updates

deepTools

a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

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.

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

ProPhyle

ProPhyle is an accurate, resource-frugal and deterministic phylogeny-based metagenomic classifier.

Pangolin-DL

a deep-learning based method for predicting splice site strengths.

HiCExplorer

is a set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data.

AWS CLI

(Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.

goleft

goleft is a collection of bioinformatics tools written in go distributed together as a single binary.

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.

Cutadapt

finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

breseq

a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.

locarna

Tools for the structural analysis of RNA

Sniffles

a structural variation caller using third generation sequencing.

SeqFu

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

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.

Balrog

A universal protein model for prokaryotic gene prediction

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.

bamtofastq

Tool for converting 10x BAMs produced by Cell Ranger

bfc

a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data.

Bismark

a set of tools for the time-efficient analysis of Bisulfite-Seq (BS-Seq) data. Bismark performs alignments of bisulfite-treated reads to a reference genome and cytosine methylation calls at the same time.

Ghostscript

an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.

Foldseek

a program that enables fast and sensitive comparisons of large structure sets.

Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

arcasHLA

high-resolution HLA typing from RNA seq.

Infernal

(INFERence of RNA ALignment) a program that searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

Flye

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