De Bruijn assembly method for Illumina, SOLiD System, and Ion Torrent data
The De Bruijn assembly method for Illumina, SOLiD System, and Ion Torrent data uses short words instead of entire reads as indices to develop the De Bruijn graph, which reduces redundancy. The software scans the reads for the first occurrence of each short word and records the location of the short word in the read. After the location of each short word in the reads is recorded, each read is represented by the short words that it contains and by its overlaps with other reads to create an index table. Reads are then mapped as a path along the graph with nodes representing overlaps and arcs between nodes representing links.
Setting | Description |
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Index Size | The length of the sequence (short word) that is used in the index table for assembly. The value must be an odd integer in the 17 - 99 range. Shorter reads require a smaller index size. For example, reads of 36 bp might work well with an index size = 21. Note: The smaller the index size, the more computer memory is required to process the index. |
Paired Reads Data - Available for datasets that were generated by paired reads. |
• Library Size | • The size of the fragment that was generated for sequencing from both ends. |
• Expected Coverage | • The average depth of coverage in reads at any single position within the reference. |