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• Introduction
  • Overview of Commands
    • Core analysis tools
    • Reporting tools overview
    • Assemblies post-processing tools
    • Sequences preparation tools
    • Format conversion
  • Latest improvements
• 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 the CLC Network License Manager
    • 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
  • References and indexes
  • Reads
    • Single reads
    • Paired reads
  • Alignment parameters
    • Match score
    • Mismatch cost
    • Linear gap cost
    • Affine gap cost
    • Alignment mode
  • Reporting and filtering
  • Quality filtering
• 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
    • AGP export
    • Bubble resolution
    • Converting the graph to contig sequences
    • Summary
  • Randomness in the results
  • Specific characteristics of CLC 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
  • New long read assembly tools (beta)
  • The clc_correct_pacbio_reads tool (beta)
    • Interlude: Converting PacBio's BAM to FASTA
    • Basic usage
    • Advanced parameters
  • The clc_assembler_long tool (beta)
    • Method
    • Input parameters
    • Graph construction
    • Graph post-processing
    • Contig post-processing
    • Output parameters
    • An example including error-correction for PacBio reads
• Reporting tools
  • The clc_sequence_info Program
  • The clc_mapping_table Program
  • The clc_mapping_info Program
• Assembly post-processing tools
  • The clc_change_cas_paths Program
  • The clc_filter_matches Program
  • The clc_extract_consensus 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
  • The clc_agp_join Program
• Sequence preparation tools
  • The clc_adapter_trim Program
  • Quality trimming
    • Fastq quality scoring
  • The clc_remove_duplicates Program
    • 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
• Options for All Programs
  • Options for clc_adapter_trim
  • Options for clc_agp_join
  • Options for clc_assembler
  • Options for clc_assembler_long
  • Options for clc_cas_to_sam
  • Options for clc_change_cas_paths
  • Options for clc_convert_sequences
  • Options for clc_correct_pacbio_reads
  • Options for clc_extract_consensus
  • Options for clc_filter_matches
  • 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_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
• Third Party Libraries
• Bibliography

The Basics

The chapter covers the basics of command line use in CLC Assembly Cell, including data format considerations such as supported data formats, the cas assembly file format and conversion to other assembly formats. The chapter ends with an overview of paired data handling in CLC Assembly Cell.

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Subsections

• How to use the programs
• Input Files
• Cas File Format
• Paired read Considerations

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