Trace formatting - Revision history

Dpuiu: /* Articles */

2011-07-20T14:19:34Z

Articles

← Older revision		Revision as of 14:19, 20 July 2011
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	* [http://www.ncbi.nlm.nih.gov/pubmed/19133817?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Short-Read Sequencing Technologies for Transcriptional Analyses.]		* [http://www.ncbi.nlm.nih.gov/pubmed/19133817?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Short-Read Sequencing Technologies for Transcriptional Analyses.]
	* [http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html Next Generation Sequencing - Bioinformatics Journal - Virtual Edition]		* [http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html Next Generation Sequencing - Bioinformatics Journal - Virtual Edition]

	* [http://www.sciencemag.org/products/lst_20090410.dtl Sanger Who Science April 2009]		* [http://www.sciencemag.org/products/lst_20090410.dtl Sanger Who Science April 2009]
			* [http://genome.cshlp.org/content/early/2011/07/18/gr.123638.111.full.pdf+html?rss=1 Accurate and comprehensive sequencing of personal genomes] Genome Research July 2011

	= Cleaning =		= Cleaning =

Dpuiu: /* Pacific Biosciences */

2011-07-15T19:25:36Z

Pacific Biosciences

← Older revision		Revision as of 19:25, 15 July 2011
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	* [http://www.ncbi.nlm.nih.gov/sra/SRX032451?report=full SRX032451] SRA dataset; Sequencing for H1 (Haiti, 2010)		* [http://www.ncbi.nlm.nih.gov/sra/SRX032451?report=full SRX032451] SRA dataset; Sequencing for H1 (Haiti, 2010)
	* [http://www.pacbiodevnet.com/EColi_WF_DS Ecoli] Company dataset ; registration needed		* [http://www.pacbiodevnet.com/EColi_WF_DS Ecoli] Company dataset ; registration needed
			* http://www.genomeweb.com/informatics/pacbio-releases-open-source-analysis-suite-ahead-single-molecule-sequencer-launc

	* [http://www.pacbiodevnet.com/smrtanalysis/software/smrtanalysis smrtanalysis]		* [http://www.pacbiodevnet.com/smrtanalysis/software/smrtanalysis smrtanalysis]

Dpuiu: /* Pacific Biosciences */

2011-07-14T19:51:39Z

Pacific Biosciences

← Older revision		Revision as of 19:51, 14 July 2011
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	* [http://www.ncbi.nlm.nih.gov/sra/SRX032451?report=full SRX032451] SRA dataset; Sequencing for H1 (Haiti, 2010)		* [http://www.ncbi.nlm.nih.gov/sra/SRX032451?report=full SRX032451] SRA dataset; Sequencing for H1 (Haiti, 2010)
	* [http://www.pacbiodevnet.com/EColi_WF_DS Ecoli] Company dataset ; registration needed		* [http://www.pacbiodevnet.com/EColi_WF_DS Ecoli] Company dataset ; registration needed

			* [http://www.pacbiodevnet.com/smrtanalysis/software/smrtanalysis smrtanalysis]

	=== Megachile rotundata PacBio sequence ===		=== Megachile rotundata PacBio sequence ===

Dpuiu: /* Pacific Biosciences */

2011-07-14T17:55:22Z

Pacific Biosciences

← Older revision		Revision as of 17:55, 14 July 2011
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	* http://www.pacificbiosciences.com/newsletter_2011_05/informatics.php		* http://www.pacificbiosciences.com/newsletter_2011_05/informatics.php
	* http://www.pacbiodevnet.com/		* http://www.pacbiodevnet.com/ login
	* http://www.pacbiodevnet.com/ConversionTools		* http://www.pacbiodevnet.com/ConversionTools
	* [http://www.ncbi.nlm.nih.gov/sra/SRX032451?report=full SRX032451] SRA dataset; Sequencing for H1 (Haiti, 2010)		* [http://www.ncbi.nlm.nih.gov/sra/SRX032451?report=full SRX032451] SRA dataset; Sequencing for H1 (Haiti, 2010)

Dpuiu: /* Megachile rotundata PacBio sequence */

2011-07-11T18:55:50Z

Megachile rotundata PacBio sequence

← Older revision		Revision as of 18:55, 11 July 2011
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	** High Quality (HQ) FASTA (edited) These FASTA files are similar to the ones described above, but have been filtered and edited. Here, the SMRT bell adaptors have been excised from the parent reads, and entries have been broken into corresponding sub-reads. Only reads with a quality filter of 75% or better have been retained; sub-reads less than 50 nt in length have been removed. These are still single pass representations of the sequence reads and therefore contain uncorrected errors, insertions, and deletions incidental to the current state of the PacBio technology.		** High Quality (HQ) FASTA (edited) These FASTA files are similar to the ones described above, but have been filtered and edited. Here, the SMRT bell adaptors have been excised from the parent reads, and entries have been broken into corresponding sub-reads. Only reads with a quality filter of 75% or better have been retained; sub-reads less than 50 nt in length have been removed. These are still single pass representations of the sequence reads and therefore contain uncorrected errors, insertions, and deletions incidental to the current state of the PacBio technology.

			** [[Media:SMRT_Pipe_Reference_Guide.pdf]]

	== Visigen ==		== Visigen ==

Dpuiu: /* Pacific Biosciences */

2011-07-11T18:50:57Z

Pacific Biosciences

← Older revision		Revision as of 18:50, 11 July 2011
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	* http://www.pacbiodevnet.com/		* http://www.pacbiodevnet.com/
	* http://www.pacbiodevnet.com/ConversionTools		* http://www.pacbiodevnet.com/ConversionTools
			* [http://www.ncbi.nlm.nih.gov/sra/SRX032451?report=full SRX032451] SRA dataset; Sequencing for H1 (Haiti, 2010)
			* [http://www.pacbiodevnet.com/EColi_WF_DS Ecoli] Company dataset ; registration needed

	* SRA dataset :		=== Megachile rotundata PacBio sequence ===
	~~[http://www.ncbi.nlm.nih.gov/sra/SRX032451?report~~=~~full SRX032451] Sequencing for H1 (Haiti, 2010)~~
	* Company dataset:
	~~[http://www.pacbiodevnet.com/EColi_WF_DS Ecoli] registration needed~~

	* Megachile rotundata: PacBio sequence
	** HDF5 (http://www.hdfgroup.org/HDF5/) This is PacBio's native data format, used to feed their primary and secondary pipelines. There is almost no support for this format outside of PacBio's analysis pipeline. Subsets of this data may be generated, however, as indicated below (e.g., FASTA and FASTQ format). According to the documentation (attached) for PacBio's hybrid assembly protocol (HybridAssembly) you may use HDF5 or FASTA in conjunction with Illumina-based scaffolds (or assembly-rpoduced contigs.)		** HDF5 (http://www.hdfgroup.org/HDF5/) This is PacBio's native data format, used to feed their primary and secondary pipelines. There is almost no support for this format outside of PacBio's analysis pipeline. Subsets of this data may be generated, however, as indicated below (e.g., FASTA and FASTQ format). According to the documentation (attached) for PacBio's hybrid assembly protocol (HybridAssembly) you may use HDF5 or FASTA in conjunction with Illumina-based scaffolds (or assembly-rpoduced contigs.)

Dpuiu: /* Pacific Biosciences */

2011-07-11T18:49:55Z

Pacific Biosciences

← Older revision		Revision as of 18:49, 11 July 2011
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	* Company dataset:		* Company dataset:
	[http://www.pacbiodevnet.com/EColi_WF_DS Ecoli] registration needed		[http://www.pacbiodevnet.com/EColi_WF_DS Ecoli] registration needed

			* Megachile rotundata: PacBio sequence
			** HDF5 (http://www.hdfgroup.org/HDF5/) This is PacBio's native data format, used to feed their primary and secondary pipelines. There is almost no support for this format outside of PacBio's analysis pipeline. Subsets of this data may be generated, however, as indicated below (e.g., FASTA and FASTQ format). According to the documentation (attached) for PacBio's hybrid assembly protocol (HybridAssembly) you may use HDF5 or FASTA in conjunction with Illumina-based scaffolds (or assembly-rpoduced contigs.)

			** High Quality (HQ) FASTA/FASTQ (post-primary analysis) We can derive from the HDF5 file FASTA and FASTQ sequences for reads passing primary analysis in the PacBio pipeline. These reads have essentially been "okayed" by the pipeline as high quality reads to carry forward in secondary analysis--such as attempted alignment to a reference genome, etc. These reads have not had PacBio's proprietary SMRT bell adaptor (45 nt x 2) trimmed... as trimming is part of the downstream PacBio secondary analysis pipeline. These are single pass representations of the sequence reads and therefore contain uncorrected errors, insertions, and deletions incidental to the current state of the PacBio technology. The FASTQ files have PacBio's "Phred-like" quality values corresponding to the nucleotide representation of the sequence. In the instances where a SMRT bell molecule is sequenced multiple times (i.e., multiple passes) each pass is termed a "sub-read". In this representation of the data, sub-reads have not been broken out from the parent sequence.

			** High Quality (HQ) FASTA (edited) These FASTA files are similar to the ones described above, but have been filtered and edited. Here, the SMRT bell adaptors have been excised from the parent reads, and entries have been broken into corresponding sub-reads. Only reads with a quality filter of 75% or better have been retained; sub-reads less than 50 nt in length have been removed. These are still single pass representations of the sequence reads and therefore contain uncorrected errors, insertions, and deletions incidental to the current state of the PacBio technology.

	== Visigen ==		== Visigen ==

Dpuiu: /* Pacific Biosciences */

2011-06-16T18:23:22Z

Pacific Biosciences

← Older revision		Revision as of 18:23, 16 June 2011
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	* http://www.pacificbiosciences.com/newsletter_2011_05/informatics.php		* http://www.pacificbiosciences.com/newsletter_2011_05/informatics.php
	* http://www.pacbiodevnet.com/		* http://www.pacbiodevnet.com/
	~~LoginEmail~~ : ~~dpuiu@umiacs~~.~~umd~~.~~edu~~		* http://www.pacbiodevnet.com/ConversionTools

	* SRA dataset :		* SRA dataset :

Dpuiu: /* Ion Torrent */

2011-06-16T15:32:25Z

Ion Torrent

← Older revision		Revision as of 15:32, 16 June 2011
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	== Ion Torrent ==		== Ion Torrent ==

	* [http://www.ncbi.nlm.nih.gov/sra/SRX067313?report=full Escherichia coli O104:H4 str. TY-2482]		* [http://www.ncbi.nlm.nih.gov/sra/SRX067313?report=full SRA Escherichia coli O104:H4 str. TY-2482]
			* [http://ioncommunity.iontorrent.com/docs/DOC-1516 Company Escherichia coli O104:H4 str. TY-2482]

	* SImilar to 454; indel & homopolimer issues		* SImilar to 454; indel & homopolimer issues

Dpuiu: /* Pacific Biosciences */

2011-06-16T15:24:56Z

Pacific Biosciences

← Older revision		Revision as of 15:24, 16 June 2011
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	* SRA dataset :		* SRA dataset :
	[http://www.ncbi.nlm.nih.gov/sra/SRX032451?report=full SRX032451] Sequencing for H1 (Haiti, 2010)		[http://www.ncbi.nlm.nih.gov/sra/SRX032451?report=full SRX032451] Sequencing for H1 (Haiti, 2010)
			* Company dataset:
			[http://www.pacbiodevnet.com/EColi_WF_DS Ecoli] registration needed

	== Visigen ==		== Visigen ==