Novocraft

Novocraft maps short reads from Illumina and SOLiD sequencing to reference genomes to enable accurate single nucleotide variant (SNV) and microindel detection in deep short-read sequencing data.

Key Features:

• Short-read mapping: Aligns Illumina and SOLiD short reads to reference genomes and was evaluated against MAQ, Bowtie, Burrows-Wheeler Alignment Tool (BWA), and RazerS.
• Microindel detection: Detects small insertions and deletions typically less than 4 base pairs in length.
• Error rate analysis and gapped alignments: Implements gapped alignments to reduce systematic SNV-calling errors that arise from ungapped alignments.
• Equivalent Indel Region (eir) algorithm: Computes equivalent indel regions by processing alignments produced by various mapping tools to facilitate accurate indel calling.
• Benchmarking with simulated datasets: Uses simulated indel-containing datasets to assess performance and compare mapping tool behavior for indel detection.

Scientific Applications:

• Resequencing and variant detection: Enhances identification of SNVs and microindels in resequencing studies using short-read data.
• Comparative genomics and platform comparison: Identifies overlapping and distinct microindels relative to ABI Sanger and Roche 454 sequencing to compare variant calls across technologies.

Methodology:

Performs systematic analysis using simulated datasets containing indels, evaluates performance across different mapping tools, applies gapped alignments to mitigate SNV-calling errors from ungapped alignments, and computes equivalent indel regions using the eir algorithm.