Novocraft A series of programs designed for accurate and high speed alignment of short reads to reference genomes.
Download

Novocraft Ranking & Summary

Novocraft Tags

display visualize genome visualize genome genome alignment display genome

Novocraft Description

A series of programs designed for accurate and high speed alignment of short reads to reference genomes. Novocraft is a package that provides a series of programs designed for accurate and high speed alignment of short reads to reference genomes. Novel features include the use of base qualities in the reads and ambiguous nucleotide codes in the reference sequences for alignment. Here are some key features of "Novocraft": Novoalign - Our aligner for single and paired end short reads: · Support for gzipped input files (Commercial Version Only, request a trial license here.) · 5' adapter stripping option (Commercial Version Only) · Multi-threaded for extra performance (Commercial Version Only) · Full index assisted Needleman-Wunsch alignment with affine gap penalties and quality based scoring · Phred style scoring and alignment qualities · Novoalign is also able to provide support for the iterative alignment process. · Indexed genome loaded into shared memory for reuse in multiprocessing · Can use fasta, fastq, solexa fastq, prb input formats. · For reads with multiple good alignments can report: none; one by random selection; or all alignments. · Also an option to report all alignments up to some maximum phred score P(R|Ai) · Posterior alignment probability (Quality Score) and filter. · Supports lower case masking of genome. · Supports varying read lengths · Adapter stripping for small RNA reads · Iterative read trimming · Integration with MAQ using 'novo2maq' · Full Needleman-Wunsch on both ends. Both ends can have gaps. · Accepts a structural variation penalty and the best alignment may be two independent ends if total score with SV penalty is better than the best pair that fits the fragment length distribution. · Initial fragment length size entered as mean and standard deviation. After this the program learns from actual fragment lengths of high quality pairs, gradually adjusting fragment length distribution and penalties to match real alignments. · This aligner is not suitable for reads from 454 or ABI Solid. Novobarcode (beta) - Novobarcode classifies reads according to "barcode" tags : · Classification uses base quality values. · Can classity PRB, FASTA, or FASTQ format reads. · Can classify single end or paired end reads. Novo2maq - A conversion utility for converting Novoalign reports into Maq map format: · This tool is based on Maq source code and provided as source files. It enables use of maq utilities for post alignment processing. · Novoindex - Novoindex builds a k-mer index of a set of reference sequences that are then the target for the alignment programs. · The reference sequence is encoded 4-bits per base in the index. The index structure retains, and redundantly indexes, up to two IUB ambiguous codes per k-mer. This is especially useful in some plant and microbial genomes that have a significant proportion of ambiguous NA codes. · A lower case masking option limits k-mer indexing to upper case NA codes. Alignments, especially paired end can extend into lower case regions. · Where memory usage is critical the index can skip k-mers with no impact on alignment sensitivity. For instance it's possible to index only every 5th 14-mer. This enables an index of the Human genome to be built in 6Gbytes or less of RAM. (k=14, s=3) · Sensitivity and specificity of the alignment programs are not affected by the index k-mer length. What's New in This Release: · Improved accuracy of quality scores for paired end reads.

Novocraft Related Software