Our aligner for  short nucleotide space reads. 

  License Type
Feature Free         Licensed
Aligns Single End, Paired End and Mate Pair libraries from Illumina/Solexa sequencers  Yes  Yes
Aligns paired end reads from 454  Yes  Yes
Adapter trimming for short RNA  Yes  Yes
Base quailities used thoughout alignment process for high statistical accuracy  Yes  Yes
Supports reads in fasta, fastq, qseq and prb formats  Yes  Yes
Supports qualities in Solexa, Illumina of Sanger formats.  Yes  Yes
For reads with multiple good alignments can report: none; one by random selection; or all alignments.  Yes  Yes
Posterior alignment probability (Quality Score) and filter.  Yes  Yes
Option for lower case masking of genome.  Yes  Yes
Allows IUB codes in reference sequence to help remove allelic bias in alignments.  Yes  Yes
Mate pair mode allows mix of paired/mate pairs and reads that cross circularisation junction  Yes  Yes
Output in industry standard SAM format  Yes  Yes
Multithreading for improved throughput    Yes
Bisulfite alignment mode for BS-Seq experiments.    Yes
Support for compressed read files, gzip or bzip2    Yes
Base quality calibration during alignment for improved sensitivity and specificity    Yes
Adapter trimming for paired end and mate pair reads.    Yes


An MPI version of Novoalign is also available. This allows multiple servers in a cluster to work together to align a file of reads.


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Last Update: 20 Oct 2014 05:13 AM