Software Updates

R

a free software environment for statistical computing and graphics.

Tracer

is a software package for visualising and analysing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. Tracer v1.7.1 can read output files from MrBayes, BEAST, BEAST2, RevBayes, Migrate, LAMARC and and possibly other MCMC programs from other domains.

BGT

is a compact file format for efficiently storing and querying whole-genome genotypes of tens to hundreds of thousands of samples. It can be considered as an alternative to genotype-only BCFv2. BGT is more compact in size, more efficient to process, and more flexible on query.

vcfanno

allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF.

GToTree

is a user-friendly workflow for phylogenomics intended to give more researchers the capability to create phylogenomic trees.

ProSolo

is a variant caller for single cell data from whole genome amplification with multiple displacement amplification (MDA). It relies on a pair of samples, where one is from an MDA single cell and the other from a bulk sample of the same cell population, sequenced with any next-generation sequencing technology.

kma

implements a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. KMA is particulary good at aligning high quality reads against highly redundant databases, where unique matches often does not exist. It works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on our users demands.

Minimap2

is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments.

yacrd

is a simple and easy to use long read error-correction tool which can detect and remove chimeras.

SeqKit

a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing.

TaxonKit

a command-line toolkit for rapid manipulation of NCBI taxonomy data.

andi

estimates the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

Mash

is a fast sequence distance estimator that uses the MinHash algorithm and is designed to work with genomes and metagenomes in the form of assemblies or reads.

FAMSA

(Fast and Accurate Multiple Sequence Aligner) implements an algorithm for large-scale multiple sequence alignments (400k proteins in 2 hours and 8BG of RAM).

trimAl

is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.

Prodigal

is a fast, reliable protein-coding gene prediction for prokaryotic genomes.

HMMER

is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

Pillow

is the friendly PIL (Python Imaging Library) fork by Alex Clark and Contributors.

The Python Imaging Library adds image processing capabilities to your Python interpreter.

This library provides extensive file format support, an efficient internal representation, and fairly powerful image processing capabilities.

The core image library is designed for fast access to data stored in a few basic pixel formats. It should provide a solid foundation for a general image processing tool.

ReportLab

is the time-proven, ultra-robust open-source engine for creating complex, data-driven PDF documents and custom vector graphics. It's free, open-source , and written in Python. The package sees 50,000+ downloads per month, is part of standard Linux distributions, is embedded in many products, and was selected to power the print/export feature for Wikipedia.

MMTF-python

(Macromolecular Transmission Format python) is the macromolecular transmission format (MMTF) binary encoding of biological structures.

SpliceV

provides analysis and publication quality printing of linear and circular RNA splicing, expression and regulation.

LoFreq

is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

MultiQC

aggregates results from bioinformatics analyses across many samples into a single report.