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- JANEWANGJK55
- http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Bowtie 2
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.
- JANEWANGJK55
- http://www.novocraft.com/main/index.php
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
- JANEWANGJK55
- 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
- JANEWANGJK55
- This seminar will provide a unique opportunity to hear leading food safety experts from the U.S. Food and Drug Administration describe the policies that have led to the implementation of a next-generation sequencing network for food pathogen traceability in the United States. They will share their experience from challenges arising from implementing the next-generation sequencing technology to real-time outbreak investigations and discuss the lessons that can be learnt to inform future policy development both here in Ireland and internationally.
Date: Monday 24th March 2014
Venue: William Jefferson Clinton Auditorium, UCD John Hume Institute for Global Irish Studies, University College Dublin, Belfield, Dublin 4
The seminar will be of interest to those working in the veterinary public health, food safety, food regulators and public health arenas, as well as those in the Irish food industry and in academia. It will provide an opportunity to gain an understanding of next-generation sequencing technology applied to traceability, outbreak tracking and public health investigations.
There is no charge to attend the workshop but places are strictly limited and we would appreciate your response to this invitation by Tuesday 18th March, 2014.
RSVP: Dr Geraldine Quinn
00 353 (0)1 716 2808
geraldine.quinn@ucd.ie
10.30 am Registration
11.00 am Opening Address: Professor Alan Reilly, CEO, Food Safety Authority of Ireland (FSAI)
Session 1: Genomic Epidemiology - The New Frontier for Molecular Subtyping. The US-FDA GenomeTrackr Project.
Chairperson: Professor Alan Reilly, CEO, Food Safety Authority of Ireland (FSAI)
11.10 am Building a National NGS Surveillance Network for Foodborne Pathogens.
Dr. Steven Musser, Deputy Centre Director Scientific Operations, U.S. Food and Drug Administration, Centre for Food Safety and Applied Nutrition, College Park, Maryland, USA.
Case Studies in Molecular Epidemiology: Source Tracking Salmonella.
Dr. Eric W. Brown, Director Division of Microbiology, U.S. Food and Drug Administration, Centre for Food Safety and Applied Nutrition, Maryland, USA.
Bioinformatics Tools and Pipelines for Real-Time Pathogen Surveillance.
Dr. Errol Strain, U.S. Food and Drug Administration, Centre for Food Safety and Applied Nutrition, College Park, Maryland, USA.
Discussion Session and Summary
Professor Alan Reilly, CEO, Food Safety Authority of Ireland (FSAI)
1.00 pm Lunch and networking
2.00 pm Session 2: Linking next-generation sequencing and data analysis – a maturing technology for real-time outbreak tracking
Chairperson: Professor Séamus Fanning, Director, UCD Centre for Food Safety
Illumina and the FDA experience – Applying MiSeq to Pathogen Tracing.
Ms. Susan Knowles, Senior Market Manager, Market Development, Illumina, Inc., Hayward, California, USA
What could you do with a 10Kb read? : SMRT sequencing for de novo bacterial assembly and methylation analysis.
Mr. Steve Picton, Director, Business Development - Europe at Pacific Biosciences, Lancaster, UK.
Bioinformatics Applications for Microbial Comparative Genomics, Gene Expression Studies and Integrated Data Analysis.
Mr. Robert Stones, The Food and Environment Research Agency, Sand Hutton, York, UK.
An Irish Experience of Whole Genome Sequencing and a Food Borne Outbreak.
Dr. Matthew McCusker, UCD Centre for Food Safety, University College Dublin, Belfield, Dublin, Ireland.
Discussion Session and Summary
Professor Séamus Fanning, Director, UCD Centre for Food Safety
