Segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, Segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, Segemehl is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gzip’ed queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.


Alignment Parameters

Number of threads/ cores to use
Parallel threads <n> will make matching much faster on machines with <n> multiple cores. Use them!
Use (multiple) split read mapping (e.g. for cDNA reads)
Segemehl supports (multiple) split read mapping. To activate the split read mapping, it is only required to give this option.
Use bisulfite mapping
Segemehl supports mapping of bisulfite-treated sequencing data where DNA fragments are treated with sodium bisulfite which results in the conversion of unmethylated cytosines into uracils while methylated cytosines remain unchanged. With bisulfite sequencing, it is possible to capture DNA methylation genomewide in an unbiased fashion with single-base resolution and is hence considered ‘gold standard’. Segemehl supports both currently used protocols for the construction of the bisulfite-treated libraries, namely methylC-seq and BS-seq.
Alignment accuracy
This option controls the minimum alignment accuracy (in percent). All reads with a best alignment below this threshold will be discarded.
Optional Parameters
For each computing step, additional parameters can be specified. For a list of all parameters, see online Segemehl user manual.

Adapter and polyA clipping

Clip 5' adapters
Using this option, Segemehl clipps adapter sequences of the 5'-ends of the reads before aligning them. Therefore you have to define a adapter sequence.
Clip 3' adapters
Using this option, Segemehl clipps adapter sequences of the 3'-ends of the reads before aligning them. Therefore you have to define a adapter sequence or in the case that you do not know the adapter sequence Segemehl can detect this sequence automatically.
Automatically clip polyA tails
Additionally, for cDNA-reads it is possible to automatically clip polyAtails . All clipping options may be combined.
Clipping accuracy [%]
You can control the clipping accuracy, selecting an integer value between 0 and 100 [%]. The default is set to 70%.
Type of clipping
All adapters and polyA-Signals will be soft-clipped. If you want hard-clipping, use this option.

Input Ports

Cell 0: Path2ReadFile1
Cell 1 (Optional): Path2ReadFile2 (if paired end mapping is used)

Output Ports

Cell 0: Path2SAMFile

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