Our aligner for Colour Space reads from the ABI SOLiD Aligner.
- Supports single end, paired end, and mate pair libraries
- Colour quality calibration.
- Support for bzipped and gzipped input files.
- Multi-threaded for extra performance.
- Phred style scoring and alignment qualities
- Can use csfasta (with qual file) & csfastq input formats.
- For reads with multiple good alignments can report: none; one by random selection; or all alignments.
- Posterior alignment probability (Quality Score) and filter.
- Quality filter for reads can remove low quality and polyclonal reads.
- Supports lower case masking of genome.
- Suports IUB ambiguous codes in reference genome to reduce allelic bias.
- Supports varying read lengths
- Iterative read trimming until read aligns
- SAM and native output formats.
An MPI version of NovoalignCS is also available. This allows multiple servers in a cluster to work together to align a file of reads.
Note. NovoalignCS and NovoalignCSMPI are only available with a license.
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