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Tool_Kits.md

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Tool Repositories, Analytical Pipelines, & Workflow Systems

ToolKits

  1. [bamtools] (https://github.com/pezmaster31/bamtools)
  • Description: command line tool kit, also API version; for reading, writing and manipulating BAM (genome alignment) files
  • Input: BAM
  • Output: BAM
  1. [Bioconductor] (http://www.bioconductor.org/)
  • Description: Open source software project, Popular R module library with over 1000 modules, can analyze diverse high-throughput genomic data; options for multiple different workflows; also available on AMI
  • Input: Multiple
  • Output: Multiple
  1. [Galaxy Tool Shed] (https://toolshed.g2.bx.psu.edu/)
  • Description: Open, web-based platform; Has 3374 valid tools for many different purposes. Looks like this site has a different tool repository for each different data type, They have agreed to support NCBI genomes, and SRA on a limited basis
  • Input: Different tools for different types of data
  • Output: Multiple
  1. [GATK] (https://www.broadinstitute.org/gatk/)
  • Description: (Broad Institute) Genome Analysis ToolKit; software library including tools (depth of coverage analyzers, quality score recalibrator, local realigner, SNP/INDEL caller), requires Ant and Java, extensive documentation and wiki system, active community, can also be used to identify somatic mutations
  • Input: Multiple
  • Output: Multiple
  1. [picard] (http://broadinstitute.github.io/picard/)
  • Description: (Broad Institute) Java based command line tools for manipulating high throughput sequencing data in the BAM format; supported through GATK
  • Input: BAM, SAM, VCF
  • Output: BAM, SAM
  1. [SAMtools] (http://samtools.sourceforge.net/)
  • Description: provides utilities for manipulating alignments in the SAM format, including sorting, merging, indexing, and generating alignments; can be used for calling SNPs and Indels
  • Input: Conforms to the specifications produced by GA4GH File Formats working group
  • Output:
  1. [VCFtools] (https://vcftools.github.io/specs.html)
  • Description: set of tools written in Perl and C++ for working with VCF files
  • Input: VCF, GZVCF, BCF
  • Output: Multiple, can be piped into another program