bioinformatics-toolbox v1.4

Full Changelog: v1.3...v1.4

bioinformatics-toolbox v1.3

• Updated the versions of the installed tools in the image
• Added metagenomics taxonomic classification tools
• Added microbiome analysis tools

Full Changelog: v1.2...v1.3

bioinformatics-toolbox v1.2

• Updated the versions of the installed tools in the image, along with upgrading the Ubuntu version to 20.04 LTS
• Removed the installed database (e.g., antiSmash) and made it optional to the user to reduce the size of the image to 20Gb
• All changes since release v1.1: v1.1...v1.2

bioinformatics-toolbox v1.1

Bioinformatics Toolbox v1.1

Tool	Description
R	The R Project for Statistical Computing
BioPerl
Biopython
NCBI BLAST+	Basic Local Alignment Search Tool
DIAMOND	Fast and sensitive protein alignment using DIAMOND
HMMER	Accelerated Profile HMM Searches
CD-HIT	CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences
MUSCLE	MUSCLE: multiple sequence alignment with high accuracy and high throughput
MAFFT	MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
JAligner	Open-source Java implementation of the Needleman–Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model
BWA	Fast and accurate short read alignment with Burrows–Wheeler transform
TopHat	Ultrafast and memory-efficient alignment of short DNA sequences to the human genome TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
HISAT2	Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Bowtie2	Fast gapped-read alignment with Bowtie 2
STAR	STAR: ultrafast universal RNA-seq aligner
Salmon	Alignment and mapping methodology influence transcript abundance estimation
kallisto	Near-optimal probabilistic RNA-seq quantification
BBMap	BBMerge – Accurate paired shotgun read merging via overlap
FASTX	Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
Trimmomatic	Trimmomatic: a flexible trimmer for Illumina sequence data
SeqKit	SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
seqtk	Toolkit for processing sequences in FASTA/Q formats
fastp	fastp: an ultra-fast all-in-one FASTQ preprocessor
HTStream	A toolset for high throughput sequence analysis using a streaming approach facilitated by Linux pipes
fqtrim	trimming & filtering of next-gen reads
TreeTime	TreeTime: Maximum-likelihood phylodynamic analysis
FastTree	FastTree 2--approximately maximum-likelihood trees for large alignments
RAxML	RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
RAxML-NG	RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
PhyML	Estimating maximum likelihood phylogenies with PhyML
Pplacer	pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
SAMtools	The Sequence Alignment/Map format and SAMtools
BCFtools	https://www.ncbi.nlm.nih.gov/pubmed/28205675
Bamtools	BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files
VCFtools	The Variant Call Format and VCFtools
BEDTools	BEDTools: a flexible suite of utilities for comparing genomic features
deepTools	deepTools2: a next generation web server for deep-sequencing data analysis
BEDOPS	BEDOPS: high-performance genomic feature operations
Sambamba	Sambamba: fast processing of NGS alignment formats
SPAdes	SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
ABySS	ABySS: a parallel assembler for short read sequence data
Velvet	Velvet: algorithms for de novo short read assembly using de Bruijn graphs
MEGAHIT	MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
MetaVelvet	MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
Prodigal	Prodigal: prokaryotic gene recognition and translation initiation site identification
Infernal	inference of RNA alignments
antiSMASH	antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters
DeepBGC	A deep learning genome-mining strategy for biosynthetic gene cluster prediction
GECCO	Accurate de novo identification of biosynthetic gene clusters with GECCO
Docker
Miniconda
CD-HIT	Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Nextflow	Nextflow enables reproducible computational workflows
GATK	The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data

bioinformatics-toolbox v1.0

bioinformatics-toolbox is a Docker container for common bioinformatics tools and programming languages.