Next

Helisphere User’s Guide

Table of Contents

1. Overview
1.1. Introduction
1.2. Release Notes
2. Installation
2.1. Prerequisites
2.2. Maintaining Multiple Installed Versions
2.3. Installing binaries
2.4. Installing from source
2.5. helicos.bashrc and HELICOS_TMPDIR
2.6. Install, Incoming and Reference Directories
2.7. Helicos Administrator
2.8. Installing the Small Examples
2.9. Installing the Big Examples
2.10. Installing References
3. Analysis Workflows
3.1. Mid Run Analysis
3.2. Full Run Oligo Analysis
3.3. Analysis of Biological Sample Channels
4. Pipelines
4.1. Overview
4.2. pypeline command
4.3. Configuration Files
4.4. Parallel Processing
4.5. oligo pipeline
4.6. midrun pipeline
4.7. basic pipeline
4.8. DGE pipeline
4.9. Resequencing pipeline
4.10. RNASeq, ChIPSeq, CNV
4.11. Extending and Creating Pipelines
5. SRF File Tools
5.1. download_srf
5.2. batch_preprocess_srf
5.3. preprocess_srf
5.4. srf2sms
6. SMS File Tools
6.1. filterSMS
6.2. extractSMS
6.3. sms2txt
6.4. smsls
7. Alignment Tools
7.1. preprocessDB
7.2. indexDPgenomic
7.3. filterAlign
7.4. sortAlign
7.5. align2sam
7.6. align2txt
7.7. align2viz
7.8. splitAlign
7.9. catAlign
7.10. templates
7.11. indexDP
8. Analysis Tools
8.1. snpSniffer
8.2. coverageTool
8.3. transcriptCount
8.4. binReads
9. Reporting Tools
9.1. lengthToolLite
9.2. lengthTool
9.3. errorTool
9.4. errorToolByCycleReport
9.5. errorToolByDetailedSubstitutionReport
9.6. errorToolByImageXYReport
9.7. errorToolByNucleotideReport
9.8. errorToolByPositionReport
9.9. errorToolDatabaseFormat
9.10. errorToolGeneralReport
10. Miscellanous
10.1. palmer
10.2. bcgen
10.3. fasta2fastq
10.4. File Formats and Extensions
10.5. Metadata in Output Text Files
11. Troubleshooting
   Next