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Last pushed: 10 months ago
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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.

  1. fastqc

    Used to run a quick check on sequencing quality

  2. fastx

    FastX_Barcode_Splitter sorts massive fastq files into smaller files based on barcode sequence

    FastX_trimmer trims barcode off sequence

  3. sickle

    Used to trim/remove reads based on quality and length

  4. samtoolsbwa

    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.

  5. picard

    Used to normalize the reference fasta file if needed

    Used to add read groups which are needed with GATK

  6. gatk3.6

    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.

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