Novel massively parallel sequencing technologies provide a highly detailed structure of transcriptome and genome by yielding deep coverage of short reads, though their utility is interfered due to a considerable sequencing quality problem and short length of reads. Sequencing-error trimming in short reads is therefore a vital process which could improve the successful rate of reference mapping as well as polymorphorism detection. Our algorithm organizes erroneous short sequences originating in a single abundant sequence into a tree structure such that each child sequence is considered to be derived stochastically from its more abundant parent sequence because of sequencing errors.

Source code

• Manual and source code of frequency-based short read clustering.
• Manual and source code of preparation for input data (Illumina).

Publication

• Efficient frequency-based de novo short read clustering for error trimming in next-generation sequencing.
  Genome Res. 2009. 19:1309-1315

Data used in the publicated paper : SRA003629

• Small RNAs of HT-29 cells
  • BAC
  • Small RNAs of HT-29 cells
  • Clustering results
  • Mapping results
• 5'-end SAGE of Dmel embryo
  • BAC
  • 5'-end SAGE of Dmel embryo cells
  • Clustering results
  • Mapping results