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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

Getting Help

This manual gives information about the tools included in CLC Assembly Cell.

Full usage information for each program is available in Appendix A of this user manual, and also by running any of the CLC Assembly Cell commands without any arguments. For the core programs, clc_mapper and clc_assembler, particular parameters are discussed in more detail within the chapters dedicated to those tools.

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