Nature focus issue - sequencing technology: http://www.nature.com/nbt/journal/v30/n11/index.html

Technologies

For a comparison of next-generation sequencing methods, see http://en.wikipedia.org/wiki/Dna_sequencing#Next-generation_methods

Sanger sequencing (chain termination method)

Pyrosequencing ("454 sequencing")

Pyrosequencing is a "sequence by synthesis" method developed by Mostafa Ronaghi and Pål Nyrén at the Royal Institute of Technology, Stockholm. Sequences are determined by observation of light emission upon addition of a nucleotide complementary to the first unpaired nucleotide of the template.

Quote from Wikipedia:Pyrosequencing:

"ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5´ phosphosulfate (APS) and luciferin."

Sequencing proceeds as follows:

Addition of one of the four dNTPs (dATPαS is substituted for ATP, as the former is not a substrate for luciferase). If the dNTP is complementary, DNA polyerase incorporates the nucleotide, releasing pyrophosphate (PPi).
ATP sulfurylase catalyzes reaction of PPi and adenosine 5' phosphosulfate to create ATP
ATP fuels luciferase-catalyzed conversion of luciferin to oxyluceferin, generating visible light.
Unincorporated nucleotides and ATP are degraded by apyrase.

454 sequencing performs massively parallel pyrosequencing. Library DNA containing adapter sequences are adsorbed to DNA-capturing beads. The DNA bound to each bead is then amplified by emulsion-PCR, in which the beads with bound DNA are mixed with PCR reagents and emulsion oil to create a water-in-oil emulsion containing many "microreactors" consisting of beads sorrounded by water. Following PCR amplification, the DNA-binding beads are isolated and deposited into the wells of a microtiter plate. Beads with pyrosequencing enzymes are then added to the plate. Finally, the pyrosequencing is performed, processing the plate in a sequencing machine. 400 000+ DNA fragments/beads can be processed per plate.

Using "multiplex identifiers", different genomic libraries can be bar-coded, facilitating sequencing of several libraries in the same sequencing run.

Platforms:

Platform	Throughput (bases/run)	Time per run	Average (a)/mode (m) read length (nt)	Accuracy	Introduced (year)
GS FLX+	700 Mbp	23h	Up to 1000	700 bp (m)
GS Junior	35Mbp	12 h	400	400 bp (a) at Phred20/read

GS FLX:

References:

Introductory paper, 454 sequencing: http://www.ncbi.nlm.nih.gov/pubmed/16056220?dopt=Abstract&holding=npg

http://www.wellcome.ac.uk/Education-resources/Education-and-learning/animations/dna/wtx056046.htm

The development and impact of 454 sequencing

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

Overview of 454 sequencing: http://classes.soe.ucsc.edu/bme215/Spring09/PPT/BME%20215-5.pdf

Illumina (Solexa) sequencing

http://www.illumina.com/technology/sequencing_technology.ilmn

Platform	Throughput (bases/run) (maximum)	Time per run	Read length (nt)	Accuracy
MiSeq Personal Sequencer	Up to 8.5 gbp	4 - 48 h	250	>70% bases higher than Q30 at read length 2 x 300 bp
HiSeq 2500/1500	600 Gb		2 x 100	>80 % higher than Q30
HiSeq 2000/1000	300 Gb		2 x 100	>80 % higher than Q30
Genome Analyzer IIx	95 Gb		2 x 150	>80 % higher than Q30

MiSeq datasheet: http://www.illumina.com/documents/products/datasheets/datasheet_miseq.pdf

Side by side comparison of Illumina sequencers: http://www.illumina.com/systems/sequencing.ilmn

Illumina - an introduction to NGS: http://www.illumina.com/Documents/products/Illumina_Sequencing_Introduction.pdf

Ion semiconductor sequencing

Ion Torrent: http://www.invitrogen.com/site/us/en/home/brands/Ion-Torrent.html?cid=fl-iontorrent Platforms:

Platform	Throughput (bases/run)	Time per run	Typical read length	Accuracy	Introduced (year)
Ion PGM sequencer	10 Mb to 1Gb	90 min+	35-400 bp
Ion Proton sequencer	1 human genome	2h+	100 bp

http://www3.appliedbiosystems.com/cms/groups/applied_markets_marketing/documents/generaldocuments/cms_096460.pdf

Nanopore sequencing

Oxford Nanopore: http://www.nanoporetech.com/

Single molecule real time sequencing (Pacific Biosciences)

Microscopical wells on a chip (zero-mode waveguides) each contain a single DNA polymerase enzyme bound to the bottom of the well, which accept a single DNA molecule as template. Fluorescent labelled dNTPs are used for DNA synthesis. Upon incorporation of a dNTP, the fluorescence tag is cleaved from the nucleotide and diffuses from the observation area within the ZMW. The sequence is determined optically by observing incorporation events.

http://www.pacificbiosciences.com/

Platforms:

PacBio RS:

http://www.pacificbiosciences.com/products/

http://www.pacificbiosciences.com/brochure

http://www.pacificbiosciences.com/pdf/Software_and_Analysis_Brochure.pdf

SOLiD sequencing (Applied Biosystems)

DNA nanoball sequencing

http://www.completegenomics.com/services/technology/

Concepts

De Bruijn graph

http://en.wikipedia.org/wiki/De_Bruijn_graph

See also Compeaou et al. 2001, Nature Biotechnology - How to apply de Bruijn graphs to genome assembly: http://www.nature.com/nbt/journal/v29/n11/full/nbt.2023.html

Bridge amplification

http://seq.molbiol.ru/sch_clon_ampl.html

RNA-Seq

Genotyping by Sequencing (GBS)

http://www.maizegenetics.net/gbs-overview

ROC

See http://en.wikipedia.org/wiki/Receiver_operating_characteristic

Edit distance

See http://en.wikipedia.org/wiki/Levenshtein_distance

Color Space/2-base encoding

See

http://finchtalk.geospiza.com/2008/03/color-space-flow-space-sequence-space.html

http://www.biostars.org/p/43855/

http://marketing.appliedbiosystems.com/images/Product_Microsites/Solid_Knowledge_MS/pdf/CSHL_Fu.pdf

Targeted sequencing

Targeted "capturing kits" may be used to sequence a subset of genomic DNA. The human exome (as defined by the Consensus CDS (CCDS) project) totals about 38 Mb, covering about 1.22 % of the human genome

(The SureSelect Human All Exon Kit )

Scaffolding

http://genome.jgi-psf.org/help/scaffolds.html

http://seqanswers.com/wiki/How-to/scaffolding

http://bioinformatics.oxfordjournals.org/content/early/2012/04/05/bioinformatics.bts175

http://www.scfbm.org/content/7/1/4

http://www.cbcb.umd.edu/research/assembly_primer.shtml

Paired-end reads

N50 Statistic

N50 length: In a collection of contigs, the longest length for which the subset of contigs consisting of all contigs with that length or longer contains at least half of the total of the length of the contig collection.

NG50: As N50, except that the goal is half of the total of the genome size.

http://en.wikipedia.org/wiki/N50_statistic

http://seqanswers.com/forums/showthread.php?p=41420

Haplotypes

Loss of Heterozygosity

http://en.wikipedia.org/wiki/Loss_of_heterozygosity

Copy number variants (CNVs)

Short Tandem Repeats (STRs)

Genotyping of STRs is used to produce forensic DNA profiles. See http://massgenomics.org/2013/01/identifying-samples-genomic-data.html

http://www.biology.arizona.edu/human_bio/activities/blackett2/str_codis.html

http://www.cstl.nist.gov/strbase/fbicore.htm

Databases

http://www.ncbi.nlm.nih.gov/gap

Sequence Read Archive: http://www.ncbi.nlm.nih.gov/sra

European Nucleotide Archive: http://www.ebi.ac.uk/ena/

Sequence alignment/Assembly

Compendium of HTS mappers: http://wwwdev.ebi.ac.uk/fg/hts_mappers/

Comparison of assemblers: http://lh3lh3.users.sourceforge.net/alnROC.shtml

BWA: http://bio-bwa.sourceforge.net/

Bowtie - An ultrafast memory-efficient short read aligner:' http://bowtie-bio.sourceforge.net/index.shtml

http://www.ncbi.nlm.nih.gov/pubmed/20211242

Primers and reviews:

http://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_li.pdf

NCBI primer on genome assembly methods: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/assembly.shtml

Nature Biotechnology Primer - How to map billions of short reads onto genomes: http://www.nature.com/nbt/journal/v27/n5/full/nbt0509-455.html

Bioinformatics, 2012: Tools for mapping high-throughput sequencing data: http://bioinformatics.oxfordjournals.org/content/28/24/3169

A survey of sequence alignment algorithms for next-generation sequencing: http://bib.oxfordjournals.org/content/11/5/473.full

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019175

De novo assembly:

Optimal Assembly for High Throughput Shotgun Sequencing: http://arxiv.org/abs/1301.0068

Counter-intuitevely, too high coverage can be problematic: http://seqanswers.com/forums/showthread.php?t=24965

Sequencing services

Service	Sample specification	Primer specification	Ship to	Link
GATC LightRun	Add 5 uL DNA (80-100 ng/uL plasmid or 20-80 ng/uL purified PCR product) + 5 uL 5uM (5 pmol/uL) primer to the same tube	Tm 52-58 C, 17-19 bp, (8-9 G+C for 18-mer) G or C at 3' end (max 3 Gs or Cs), maximum 4bp run.	GATC Biotech AG. European Custom Sequencing Centre. Gotrfied-Hagen-Strasse 20. 51105 Köln.	http://www.gatc-biotech.com/en/lp4/new-lightrun-sequencing.html
Macrogen Single-pass	Add 20 uL DNA (100 ng/uL plasmid or 50 ng/uL purified PCR product) to one tube. Add 20µl primer (10 pmol/uL) to a separate tube.	18-25 bp, 40-60 % GC, Tm 55-60	Macrogen Europe, IWO, Kamer IA3-195, Meibergdreef 39,1105 AZ Amsterdam Zuid-oost. Netherlands. Attention: J.S .Park.	http://dna.macrogen.com/eng/support/seq/seq_submission.jsp

Sequencing-based techniques

ChIP-sequencing

Sequencing/genomics centres

BGI: http://www.genomics.cn/

New York Genome Center: http://nygenome.org/

JGI: http://www.jgi.doe.gov/

Primers

Custom primers

Name	Length (bp)	Sequence	Tm (C) [calculated]	Tm (C) [Analytical]	GC (% / bp)	Comment
pJP-1_seq5	18	CAGCGTGCGAGTGATTAT	53.9/60.6 (2)/52.6 (3)	50		Binds upstream of XylS region in pSB-M1g
pJP-1_seq6	18	AGACCACATGGTCCTTCT	57.5° (2)/52.8 ºC(3)	53.9	50	Binds near end of GFPmut3 in pSB-M1g
SeqMG1		AGCAGATCCACATCCTTGAA	62.7 (2)/53.7 (3)			Binds at nt 5672 of pSB-M1g, upstream of AgeI site. Designed to Macrogen sequencing primer criteria.
pSB-SeqA	18	TGCAAGAAGCGGATACAG	56 / 60.7°C (2)/52.3 ºC (3)		50	Binds at nt 7729 of pSB-M1g, upstream of Pm promoter and PciI site.

Universal primers

http://www.generi-biotech.com/sequencing-universal-seguencing-primers/ http://www.synthesisgene.com/tools/Universal-Primers.pdf http://www.genewiz.com/public/universalprimers.aspx https://secure.eurogentec.com/product/research-universal-primers.html

Tm calculations: 1: CloneManager 2: Thermo Scientific 3: IDT Oligoanalyzer

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers http://www.biomedcentral.com/1471-2164/13/341

Software

Chromatogram viewers: http://www.dnaseq.co.uk/chrom_view.html

CodonCode aligner: http://www.codoncode.com/aligner/

BioEdit: http://www.mbio.ncsu.edu/BioEdit/bioedit.html

FinchTV: http://www.geospiza.com/Products/finchtv.shtml

About SCF (sequence chromatogram format) files: http://staden.sourceforge.net/manual/formats_unix_2.html

https://wiki.nci.nih.gov/display/TCGA/Sequence+trace+files

http://code.google.com/p/seqtrace/

http://www.phrap.com/background.htm

http://en.wikipedia.org/wiki/Phrap

http://www.ncbi.nlm.nih.gov/books/NBK47537/

http://www.bio.net/bionet/mm/autoseq/1999-April/001368.html

High-throughput sequencing tools:

SAM tools: http://samtools.sourceforge.net/

Burrows-Wheeler Aligner (BWA): http://bio-bwa.sourceforge.net/

http://seqanswers.com/wiki/BWA

Maq: Mapping and Assembly with Qualities

Sequencing quality and standards:

http://www.phrap.com/phred/

http://www.bio.net/bionet/mm/autoseq/1999-April/001366.html

http://en.wikipedia.org/wiki/Phred_quality_score

Sequencing projects

File formats

Sequence Alignment/Map (SAM) format: "A generic format for storing large nucleotide sequence alignments". Tab-delimited text format consisting of a header section (optional) and an alignment section.

http://samtools.sourceforge.net/

http://samtools.sourceforge.net/SAM1.pdf