pradosj/ngs repository overview

The current version include:

• samtools 1.3.1
• bcftools 1.3.1
• htslib 1.3.2
• bwa 0.7.15
• bowtie 2.2.9
• tophat 2.1.1
• cuffdiff 2.1.1
• sga 0.10.15
• STAR 2.5.2b
• picard-tools
• HTSeq
• MACS2

Example usage to map contigs onto a reference genome with BWA mem.

docker run --rm -v $(pwd):/export pradosj/ngs 'bwa index ref.fa && bwa mem -t4 ref.fa contigs.fasta | samtools view -Sb - | samtools sort -o contigs.bam - && samtools index contigs.bam'