bioinformatics-toolbox - bioinformatics-toolbox v1.4

Full Changelog: https://github.com/ahmedmoustafa/bioinformatics-toolbox/compare/v1.3...v1.4

- Dockerfile
Published by ahmedmoustafa over 1 year ago

bioinformatics-toolbox - 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: https://github.com/ahmedmoustafa/bioinformatics-toolbox/compare/v1.2...v1.3

- Dockerfile
Published by ahmedmoustafa over 2 years ago

bioinformatics-toolbox - 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: https://github.com/ahmedmoustafa/bioinformatics-toolbox/compare/v1.1...v1.2

- Dockerfile
Published by ahmedmoustafa about 3 years ago

bioinformatics-toolbox - 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 |

- Dockerfile
Published by ahmedmoustafa over 4 years ago

bioinformatics-toolbox - bioinformatics-toolbox v1.0

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

- Dockerfile
Published by ahmedmoustafa over 4 years ago