Manuals
Browse the manual
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
Restricting CPU usage
All the assembly programs can be restricted on the number of CPUs to use. The `-cpus' option is used for this purpose and will define the maximum number of CPUs to use.
