Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
Novocraft Technologies is a bioinformatics company specializing in
the development of fast and accurate tools for next-generation sequencing (NGS) analysis and,
provision of bioinformatics services where our team of experts analyse your NGS data for you.
Our primary product is an aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.
No limit of 2 mismatches per read, aligns with up to 8 or more mismatches per read, up to 16 on paired end reads.
Gapped alignment on single end reads and paired end reads. Gaps up to 7bp on single end reads, even longer on paired end reads.
Uses base qualities at all steps in the alignment for greater accuracy.
Native SAM/BAM alignment output format
Single pass alignment for Bisulphite treated DNA.
Base Quality calibration for greater accuracy and extra reads. Do you still need the phiX control lane?
3' & 5' Adapter stripping for short fragments (eg. miRNA) & PCR adapters
Pooled samples with indexing using Novobarcode.
Excellent performance on long reads from the Illumina GA II
Cluster-aware message passing interface (MPI) and multithreaded versions
Align Illumina Mate pairs including: mixed pairs/mates, and split ends when read includes circularisation junction
Align 454 paired end reads