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• Introduction
  • Overview of Commands
    • Core analysis tools
    • Viewing and reporting tools
    • Assembly post-processing tools
    • Sequence preparation tools
    • Format conversion
• System Requirements and Installation
  • System requirements
    • Limitations on maximum number of cores
    • Supported CPU architectures
  • Disk space
  • Downloading and installing the software
  • Installing Static license
    • Licensing the software on a networked Linux or Mac machine
    • Licensing the software on a networked Windows machine
    • Licensing the software on a non-networked machine
  • Network Licenses
    • Installing and Running CLC License Server
    • Configuring the software to use a network license
  • Restricting CPU usage
• The Basics
  • How to use the programs
    • Getting Help
    • A basic example
  • Input Files
  • Cas File Format
    • Cas Format Basics
    • What a cas file contains
    • What a cas file does not contain
    • Considerations and limitations
    • Converting to and from SAM and BAM formats
  • Paired read Considerations
    • Relative orientation of the reads
    • Measuring the distance between the reads
    • Paired Read File Input
• Read Mapping
  • Overview of base space mapping
  • Circular references
  • Saving and re-using reference index files
  • Overview of color space mapping
    • Sequencing
    • Error modes
    • Mapping in color space
    • Color space file formats
  • General information for both read mappers
    • Non-specific matches
    • Placement of Read Pairs
    • Scoring Schemes
    • Mapping quality thresholds
  • Running Read Mapping Analyses
  • Mixed base space and color space mappings
• De novo assembly
  • De novo assembly inputs
  • De novo assembly outputs
  • How it works
    • Resolve repeats using reads
    • Automatic paired distance estimation
    • Optimization of the graph using paired reads
    • Bubble resolution
    • Converting the graph to contig sequences
    • Summary
  • Randomness in the results
  • Specific characteristics of CLC bio's algorithm
  • SOLiD data support in de novo assembly
  • Command line options
    • Specifying the data for the assembly and how it should be used
    • Specifying information for the assembly
    • Specifying information about the outputs
    • Other options
    • Example commands
• Viewing and reporting tools
  • Assembly Viewer
  • The clc_sequence_info Program
  • The clc_mapping_table Program
  • The clc_mapping_info Program
• Assembly post-processing tools
  • The change_cas_paths Program
  • The clc_filter_matches Program
  • The clc_find_variations Program
  • The clc_join_mappings Program
  • The clc_submapping Program
    • Specifying Mapping Files
    • Extracting a Subset of Reference Sequences
    • Extracting a Part of a Single Reference Sequence
    • Extracting Only Long Contigs (Useful for De Novo Assembly)
    • Extracting a Subset of Read Sequences
    • Other Match Restrictions
    • Output Reference File
    • Output Read File
    • Handling of non-specific matches
  • The clc_unmapped_reads Program
  • The clc_unpaired_reads Program
• Sequence preparation tools
  • The clc_adapter_trim Program
  • Quality trimming
    • Fastq quality scoring
  • The clc_remove_duplicates
    • Looking for neighbors
    • Sequencing errors in duplicates
    • Paired data
    • Known limitations
    • Example of duplicate read removal
  • The clc_sample_reads Program
  • The clc_sort_pairs Program
  • The clc_split_reads Program (for 454 paired data)
  • The clc_overlap_reads Program
• Format conversion tools
  • The clc_cas_to_sam Program
  • The clc_sam_to_cas Program
  • The clc_convert_sequences Program
• Updating program names from earlier versions
• Options for All Programs
  • Options for change_clc_names
  • Options for clc_adapter_trim
  • Options for clc_assembler
  • Options for clc_cas_to_sam
  • Options for clc_change_cas_paths
  • Options for clc_convert_sequences
  • Options for clc_filter_matches
  • Options for clc_find_variations
  • Options for clc_join_mappings
  • Options for clc_mapper
  • Options for clc_mapper_legacy
  • Options for clc_mapping_info
  • Options for clc_mapping_table
  • Options for clc_mapping_viewer
  • Options for clc_name_changes.txt
  • Options for clc_overlap_reads
  • Options for clc_quality_trim
  • Options for clc_remove_duplicates
  • Options for clc_sample_reads
  • Options for clc_sam_to_cas
  • Options for clc_sequence_info
  • Options for clc_sort_pairs
  • Options for clc_split_reads
  • Options for clc_submapping
  • Options for clc_unmapped_reads
  • Options for clc_unpaired_reads
• Bibliography

Command line options

This section provides details of the command line options available for the clc_assembler command. As with all other programs in the CLC Assembly Cell, full usage information are given in Options and can be viewed by executing the command without any arguments.

Note that you can use the clc_sequence_info program with the `-n' option to get statistics on the result of a de novo assembly. This is described in the Viewing and reporting tools section of the manual.

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Subsections

• Specifying the data for the assembly and how it should be used
• Specifying information for the assembly
• Specifying information about the outputs
• Other options
• Example commands

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