This repository contains several Dockerfile for building Docker container images of bioinformatics tools (read filtering and alignment, feature count, R and Bioconductor). Each directory for one tool. Inside each directory there are many directories representing a tool version. The version must be equal to tool version defined in Dockerfile. Dockerfiles are tagged according to tool version.
| Tool | Description |
|---|---|
| admixture | Software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets |
| bcl2fastq | Demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats |
| Bioconductor | Provides tools for the analysis and comprehension of high- throughput genomic data |
| Bismark | Maps bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step |
| Bowtie | An ultrafast, memory-efficient short read aligner |
| Bowtie 2 | An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences |
| BWA | Burrows-Wheeler Aligner |
| Cutadapt | Removes adapter sequences from sequencing reads |
| FastQC | A quality control tool for high throughput sequence data |
| fineSTRUCTURE | Fast and powerful algorithm for identifying population structure using dense sequencing data |
| GATK | Genome Analysis Toolkit - Variant Discovery in High-Throughput Sequencing Data |
| HTSeq | Counting reads in features |
| Reaper | Program for demultiplexing, trimming and filtering short read sequencing data |
| Picard | A set of command line tools for manipulating high-throughput sequencing data |
| Plink | Whole genome association analysis toolset |
| R | Language and environment for statistical computing and graphics |
| Rqc | Quality Control Tool for High-Throughput Sequencing Data |
| Samtools | Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format |
| Shapeit2 | Fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data |
| STAR | RNA-seq aligner |
| featureCounts | Counting reads to genomic features such as genes, exons, promoters and genomic bins |
| TrimGalore! | A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files |
| VCFTools | Program package designed for working with VCF files |
Build Docker images and push to DockerHub
The command below builds and pushes Docker images to DockerHub. Images are tagged with tool versions.
bash build_images.sh