Set of bioinformatics tools within docker containers to allow portability and use on any platform capable of running docker. Primary purpose of these tools has been to identify SNPs in illumina sequencing data.
Used to run a quick check on sequencing quality
FastX_Barcode_Splitter sorts massive fastq files into smaller files based on barcode sequence
FastX_trimmer trims barcode off sequence
Used to trim/remove reads based on quality and length
Contains both BWA and SAM tools to allow scripting to pass results from BWA directly into SAM tools
Allows the generation of indices for reference sequence
Aligns all reads to reference sequence
Converst sam files to bam files
Sorts the alignments
Used to index the bam files after read groups have been added.
Used to normalize the reference fasta file if needed
Used to add read groups which are needed with GATK
Used to identify sequence variants
Used to begin filtering the identified variants
Varscan not tested
samtools and bwa are also separate if want to change process.