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 |
NovoalignMPI
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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