Software Updates

Nextflow

Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data.

It is designed around the idea that the Linux platform is the lingua franca of data science. Linux provides many simple but powerful command-line and scripting tools that, when chained together, facilitate complex data manipulations.

Nextflow extends this approach, adding the ability to define complex program interactions and a high-level parallel computational environment based on the dataflow programming model.

A Nextflow script is defined by composing many different processes. Each process can be written in any scripting language that can be executed by the Linux platform (BASH, Perl, Ruby, Python, etc), to which is added the ability to coordinate and synchronize the processes execution by simply specifying their inputs and outputs.

Snakemake

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.

seqtk

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.

VSEARCH

VSEARCH is an alternative to the USEARCH tool developed by Robert C. Edgar (2010).

VSEARCH 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.

samblaster

samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file.

UCSC Tools

The UCSC tool suite contains utilities designed to work with UCSC Genome Browser data and databases.

Sambamba

Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Because of its efficiency is an important work horse running in many sequencing centres around the world today.

Bioconductor

tools to analyze and comprehend high-throughput genomic data.

Pysam

a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the SAMtools and BCFtools packages.

Pysam is installed as a module within python.

Picard

a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.

QUAST

QUAST evaluates genome assemblies by computing various metrics, including N50 length, for which the collection of all contigs of that length or longer covers at least 50% of assembly length, gNG50, where length of the reference genome is being covered, NA50 and NGA50, where aligned blocks instead of contigs are taken, misassemblies, misassembled and unaligned contigs or contigs bases, genes and operons covered. QUAST builds convenient plots for different metrics; cumulative contigs length, all kinds of N-metrics, genes and operons covered and GC content.

Cromwell

Cromwell is a Workflow Management System geared towards scientific workflows.

inDrops

Pipeline for processing inDrops sequencing data.

HHsuite

an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

Goalign

Goalign is a set of command line tools to manipulate multiple alignments. It is implemented in Go language.

Goalign aims to handle multiple alignments in Phylip, Fasta, Nexus, and Clustal formats, through several basic commands. Each command may print result (an alignment for example) in the standard output, and thus can be piped to the standard input of the next goalign command.

BEAST2

BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.

HHsuite

an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

plmc

infers undirected graphical models to describe coevolution and covariation in families of biological sequences. With a multiple sequence alignment as an input, plmc can quantify inferred coupling strengths between all pairs of positions (couplingsfile output) or infer a generative model of the sequences for predicting the effects of mutations or designing new sequences (paramfile output).

Bismark

Bismark is 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.

Gotree

GoTree is a set of command line tools to manipulate phylogenetic trees. It is implemented in Go language.

The goal is to handle phylogenetic trees in Newick, Nexus and PhyloXML formats, through several basic commands. Each command may print result (a tree for example) in the standard output, and thus can be piped to the standard input of the next gotree command.