Illumina Documentation

SolexaPipeline 0.2.2.6

• Pipeline documentation
• GERALD User Guide and FAQ

• Goat documentation - Firecrest, Bustard

• New analysis modes for GERALD in Pipeline Version 0.3

• Pipeline calibration parameters

• Pipeline FAQ

• Pipeline installation

• Pipeline IT requirements

• Pipeline output and visualisation

• Pipeline parallelisation

• Pipeline QuickStart Guide

• Pipeline releases

• Pipeline usage

• Run-Folder specification

• PE summary explanation

• PE analysis

• What do the different files in an analysis directory mean
  • Summary.htm - more detail
  • Whole genome alignments using ELAND
• Alignment Scoring Guide and FAQ
• Base-call calibration

GAPipeline 1.0

• GA2_Upgrades-new_System-Future_Enhancements.pdf
• 081014_IPAR.pdf
• SCS2.0_Events.pdf
• SCS2_01_IPAR1_01_Release_Notes.pdf
• IPAR_User_Guide_1004159_Rev_A.pdf

GAPipeline 1.3.2

• Genome_Analyzer_Software_License.pdf
• PipelineCASAVA_QRB_15001325_A.pdf
• Pipeline_CASAVA_User_Guide_1005359_A.pdf

GAPipeline 1.4

• Pipeline_CASAVA_User_Guide_15003807_A1.pdf