openrr

How to use

docker pull poulphunter/openrr:latest

To use mafft from NCBI_sequences.fasta to NCBI_sequences_aligned.fasta
With this example fasta file is in a mounted directory from host: /home/db/ source and destination is mounted in the same directory to avoid confusion.
docker run --mount type=bind,source=/home/db/,target=/home/db/ -i -t poulphunter/openrr:latest mafft --auto --thread 8 -s /home/db/NCBI_sequences.fasta > /home/db/NCBI_sequences_aligned.fasta

Tools availables

• fastqc - Quality check 

• trimmomatic - Trimming and Adapter Removal

• samtools - Pre and post processing 

• hisat2 - Alignment

• bedtools - Consensus Genome and Variant calling 

• bcftools - Consensus Genome and Variant calling

• Varscan - Consensus Genome and Variant calling

• seqtk - Consensus Genome and Variant calling

• Quast - Assembly evaluation and Statistics 

• SPAdes - de novo Genome assembly

• MEGAHIT - de novo Genome assembly 

• Krona - Evaluation of species diversity and Visualization 

• Kraken2 - Evaluation of species diversity and Visualization 

• MegaX-CC - Phylogenetic analysis 

• mafft - Phylogenetic analysis 

• fasttree - Phylogenetic analysis 

• FigTree - Phylogenetic analysis 

• BMGE ( Block Mapping and Gathering with Entropy) - Phylogenetic analysis

• system utils like : time htop screen nano curl git

Build from Dockerfile

docker build -t poulphunter/openrr .