ksimons77/samtoolsbwa repository overview

⁠NGS-Analysis

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.