CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of Next Generation Sequencing data.
Details
CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of Next Generation Sequencing data.
The command-line interface of CLC Assembly Cell enables the functionalities to be easily included in scripts and other Next Generation Sequencing work-flows.
CLC Assembly Cell is utilizing SIMD instructions to parallelize and accelerate the assembly algorithms, making the program the fastest Next Generation Sequencing assembler at present.
The main functionalities of CLC Assembly Cell are:
Read mapping
Read mapping of Illumina Genome Analyzer, SOLiD, and 454 sequencing data
Support for native Color Space assembly
Support for both short read and long read assembly, including 454/Titanium data
Support for both gapped and ungapped alignments when doing short read assemblies
Support for assembly of paired end reads
De novo assembly
De novo assembly of Illumina Genome Analyzer and 454 sequencing data
Support for both short read and long read assembly, including 454/Titanium
Support for de novo assembly of paired end data
Other analyses
Fast analysis of raw data, including reporting
Option of joining data from different sources into the same analysis (including data generated by different kinds of sequencing technologies)
Extraction of data from part(s) of an assembly. Examples are extraction of contig and reads from an area of interest, or extraction (exclusion) of data from a specific sequencing lane that is suspected not to be of acceptable quality.
Find variations (simple SNP detection)
Support for input file formats Fasta, Sff, GenBank, csfasta, and scarf
A number of output options, including tables with assembly info
A "graphical" (ASCII art :-)) assembly viewer to get quick overview
Full integration with CLC Genomics Workbench. Output data from CLC Assembly Cell can be imported and further analyzed in CLC Genomics Workbench.
Software Link: CLC Assembly Cell
Details
CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of Next Generation Sequencing data.
The command-line interface of CLC Assembly Cell enables the functionalities to be easily included in scripts and other Next Generation Sequencing work-flows.
CLC Assembly Cell is utilizing SIMD instructions to parallelize and accelerate the assembly algorithms, making the program the fastest Next Generation Sequencing assembler at present.
The main functionalities of CLC Assembly Cell are:
Read mapping
Read mapping of Illumina Genome Analyzer, SOLiD, and 454 sequencing data
Support for native Color Space assembly
Support for both short read and long read assembly, including 454/Titanium data
Support for both gapped and ungapped alignments when doing short read assemblies
Support for assembly of paired end reads
De novo assembly
De novo assembly of Illumina Genome Analyzer and 454 sequencing data
Support for both short read and long read assembly, including 454/Titanium
Support for de novo assembly of paired end data
Other analyses
Fast analysis of raw data, including reporting
Option of joining data from different sources into the same analysis (including data generated by different kinds of sequencing technologies)
Extraction of data from part(s) of an assembly. Examples are extraction of contig and reads from an area of interest, or extraction (exclusion) of data from a specific sequencing lane that is suspected not to be of acceptable quality.
Find variations (simple SNP detection)
Support for input file formats Fasta, Sff, GenBank, csfasta, and scarf
A number of output options, including tables with assembly info
A "graphical" (ASCII art :-)) assembly viewer to get quick overview
Full integration with CLC Genomics Workbench. Output data from CLC Assembly Cell can be imported and further analyzed in CLC Genomics Workbench.
Software Link: CLC Assembly Cell
