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novoSplice

novosplice_bannernovoSplice is an RNA-seq aligner which maps RNA reads to  annotated genes sequences.

Key Features:

  • Supporting Illumina, PacBio & Nanopore reads
  • Reference Indexing on-the-fly
  • Supporting references with ambiguous IUPAC base codes to reduce allelic bias
  • Utilizing bases’ quality information throughout the alignment process
  • Penalizing splice junctions differently depending on annotation support and splicing signals
  • Powered by splice- and quality-aware Needleman-Wunsch and Seed Chaining algorithms

Benchmarking

We used SimBA suite of tools to simulate RNA-seq reads and benchmark RNA-seq aligners. The simulated data sets were generated by SimCT for different species, mutation rates and read lengths. BenchCT is then called to assess the RNA-seq aligners for mapping to reference genome and discovering annotated splice junctions.We present the results of the alignment process of four different RNA-seq specialized aligners, namely STAR, HISAT2, GSNAP and novoSplice. The data sets are from three different species; Homo sapiens, Mus musculus and Danio rerio, with reads’ length equals 100 bases and number of reads around 160 million paired-end reads. danio_bench
mouse_bench danio_bench
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