Read mapping of Illumina, Pacific Biosciences, Ion Torrent, SOLiD, and 454 sequencing data
Native support for Color Space
Support for both short read and long read assembly
Support for both gapped and ungapped alignments when doing short read mapping
Support for mapping of paired end reads
De novo assembly
De novo assembly of Illumina, Pacific Biosciences, Ion Torrent and 454 sequencing data
Support for both short read and long read assembly
Support for de novo assembly of paired end data
Building scaffolds from 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.
Removal of duplicate reads
Quality trimming
Find variations (simple SNP detection)
Support for input file formats Fasta, Sff, GenBank and csfasta
A number of output options, including tables with assembly info
Full integration with Qiagen CLC Genomics Workbench and Biomedical Genomics Workbench – output data from Qiagen CLC Assembly Cell can be imported and further analyzed in Qiagen CLC Genomics Workbench and Biomedical Genomics Workbench
