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URL: https://code.google.com/p/clippers/
Proper Citation: Clippers (RRID:SCR_005256)
Description: A software program designed to identify long deletions of a genome as well as the RNA splicings using long Illumina reads. Currently, Clippers is implemented for long reads Illumina, ex: 75bp or 100bp, allowing mismatches and a single deletion/splicing. Clippers is a sister tool of PerM, our short reads aligner. Users are strongly suggested to use PerM to initially mapped reads and identify the deletion/splicing with the initially unmapped reads. We plan to extend it to ABI SOLiD reads in the near future. Clippers outputs gap-alignments in SAM format. You can use SAMtools or other program to interpret the deletion/splicing. The input files are a reference in fasta format and the reads is in fasta or fastq format.
Abbreviations: Clippers
Synonyms: clippers - Deletion Identification Program using Periodic Spaced Seed
Resource Type: software resource
Defining Citation: PMID:19675096
Keywords: long deletion, genome, rna splicing, illumina, deletion
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