Novocraft Technologies

Welcome to the Novocraft Technologies Wiki.

Here you will find a growing set of documentation on Novocraft products including user guides, performance information and reference manuals.

Contents:

• Novoalign NGS Quick Start Tutorial
  • Basic short read mapping
  • Exome sequencing analysis
  • SNP and MicroIndel detection
  • microRNA mapping
  • Novoalign SAM format validation
  • Mapping reads with Cluster-Aware NovoalignMPI
  • Demultiplexing barcoded/indexed reads with Novobarcode
  • Extracting unmapped reads from a BAM file produced by novoalign
• Novoalign User Guide
  • Getting Started
  • Adapter Stripping
    • 3 Prime Adapter Stripping
    • Paired End Short Fragment Detection and Adapter Stripping
    • PCR Adapter Stripping
  • Micro RNA
  • RNASeq analysis: mRNA and the Spliceosome
  • Bisulphite treated reads
    • Novomethyl - Analyzing Methylation Status
    • Regard the Bisulphite Treatment
  • Performance Notes
    • Long Single End Reads
    • Short vs Long Reads
    • HPCs
  • Quality Calibration
    • Bisulphite Treated DNA
    • The phiX Lane
    • Streptococcus suis Quality Calibration
  • Novoalign Command Line Options
    • Reporting Multiple Alignments per Read
    • Paired Read Modes
• NovoalignCS
• Novoindex - Indexing the Reference Genome
• Novoutil - A collection of utility functions
• Novosort
• Novo2maq
• User Contributions
  • Novopile
  • RNA_PEref - A set of perl tools to create a reference sequence set for paired end mapping of short transcriptome sequencing reads.
  • USeq Applications
• Other Sequencing Platforms
  • Helioscope Reads
  • Polonator Reads
  • 454 Paired End Reads
  • ION Torrent PGM

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