Helicobacter pylori - Revision history

Dpuiu: /* NCBI complete genomes */

2010-01-27T19:27:51Z

NCBI complete genomes

← Older revision		Revision as of 19:27, 27 January 2010
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	[[Media:NC 000915-NC 000915.20.png]], [[Media:NC 000915-NC 000915.40.png]]		[[Media:NC 000915-NC 000915.20.png]], [[Media:NC 000915-NC 000915.40.png]]

			* Repeats (NC_000915.1):
			. elem min q1 q2 q3 max mean n50 sum
			36 269 36 45 70 197 4853 305.32 1187 82132
			100 112 100 143 267 804 4853 659.07 1891 73816

	== NCBI SRA ==		== NCBI SRA ==

Dpuiu: /* CBCB */

2010-01-27T18:20:05Z

CBCB

← Older revision		Revision as of 18:20, 27 January 2010
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	Summary of what I did to assemble the 24 data sets:		Summary of what I did to assemble the 24 data sets:
	# I downloaded the read sets and 7 complete related genomes from NCBI		# I downloaded the read sets and 7 complete related genomes from NCBI : 36bp unmated reads ; original cvg range: 77-261X cvg : very deep; could be filtered
	36bp unmated reads
	original cvg range: 77-261X cvg : very deep; could be filtered
	# I ran velvet on each read set		# I ran velvet on each read set
	# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.		# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.

Dpuiu: /* CBCB */

2010-01-27T18:19:44Z

CBCB

← Older revision		Revision as of 18:19, 27 January 2010
Line 92:		Line 92:

	Summary of what I did to assemble the 24 data sets:		Summary of what I did to assemble the 24 data sets:
	# I downloaded the read sets and 7 complete related genomes from NCBI		# I downloaded the read sets and 7 complete related genomes from NCBI
	* 36bp unmated reads		36bp unmated reads
	* original cvg range: 77-261X cvg : very deep; could be filtered		original cvg range: 77-261X cvg : very deep; could be filtered
	# I ran velvet on each read set		# I ran velvet on each read set
	# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.		# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.

Dpuiu: /* CBCB */

2010-01-27T18:18:08Z

CBCB

← Older revision		Revision as of 18:18, 27 January 2010
Line 93:		Line 93:
	Summary of what I did to assemble the 24 data sets:		Summary of what I did to assemble the 24 data sets:
	# I downloaded the read sets and 7 complete related genomes from NCBI		# I downloaded the read sets and 7 complete related genomes from NCBI
	## 36bp unmated reads		* 36bp unmated reads
	## original cvg range: 77-261X cvg : very deep; could be filtered		* original cvg range: 77-261X cvg : very deep; could be filtered
	# I ran velvet on each read set		# I ran velvet on each read set
	# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.		# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.

Dpuiu: /* CBCB */

2010-01-27T18:17:52Z

CBCB

← Older revision		Revision as of 18:17, 27 January 2010
Line 92:		Line 92:

	Summary of what I did to assemble the 24 data sets:		Summary of what I did to assemble the 24 data sets:
	# I downloaded the read sets and 7 complete related genomes from NCBI (36bp unmated reads)		# I downloaded the read sets and 7 complete related genomes from NCBI
			## 36bp unmated reads
			## original cvg range: 77-261X cvg : very deep; could be filtered
	# I ran velvet on each read set		# I ran velvet on each read set
	# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.		# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.

Dpuiu: /* CBCB */

2010-01-27T18:14:44Z

CBCB

← Older revision		Revision as of 18:14, 27 January 2010
Line 92:		Line 92:

	Summary of what I did to assemble the 24 data sets:		Summary of what I did to assemble the 24 data sets:
	# I downloaded the read sets and 7 complete related genomes from NCBI		# I downloaded the read sets and 7 complete related genomes from NCBI (36bp unmated reads)
	# I ran velvet on each read set		# I ran velvet on each read set
	# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.		# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.

Dpuiu: /* CBCB */

2009-11-17T19:59:02Z

CBCB

← Older revision		Revision as of 19:59, 17 November 2009
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	== CBCB ==		== CBCB ==
	~~Reads~~ filtering:
			Summary of what I did to assemble the 24 data sets:
			# I downloaded the read sets and 7 complete related genomes from NCBI
			# I ran velvet on each read set
			# For the assemblies which were too fragmented and/or had high read coverage I filtered out the low quality reads, ran velvet on the remaining reads and see if the assembly got better. Some assemblies were better some worse.
			# I tried merging the velvet contigs based on direct overlaps (2 contig ends align to each other) or indirect overlaps (2 contigs align to the same complete genome region)
			# Velvet assemblies 6,9,18 were very fragmented so I ran AMOScmp-short reads on all the reads, using as reference the best assembled related HPKX set
			# I tried merging the velvet & AMOScmp contigs based on direct overlaps only

			----

			Read filtering:
	* q00: no reads were filter out		* q00: no reads were filter out
	* q20: reads that contained 1+ N's or had avg. quality < 20 were filtered out		* q20: reads that contained 1+ N's or had avg. quality < 20 were filtered out

Dpuiu: /* Other */

2009-11-17T19:50:54Z

Other

← Older revision		Revision as of 19:50, 17 November 2009
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	== Other ==		== Other ==
	* http://msbarker.com/software.htm		* http://msbarker.com/software.htm
			* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480403/?tool=pmcentrez The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: Evolution during disease progression] Jun 2006 PNAS
			* [http://www.jbc.org/content/284/44/30383/T1.expansion.html Response of Gastric Epithelial Progenitors to Helicobacter pylori Isolates Obtained from Swedish Patients with Chronic Atrophic Gastritis]

	= Assemblies =		= Assemblies =

Dpuiu: /* CBCB */

2009-11-09T11:43:14Z

CBCB

← Older revision		Revision as of 11:43, 9 November 2009
Line 91:		Line 91:
	* q00: no reads were filter out		* q00: no reads were filter out
	* q20: reads that contained 1+ N's or had avg. quality < 20 were filtered out		* q20: reads that contained 1+ N's or had avg. quality < 20 were filtered out
			Velvet: hash_size=23

	'''velvet''' contigs 100bp+ stats:		'''velvet''' contigs 100bp+ stats:

Dpuiu: /* CBCB */

2009-11-09T11:29:22Z

CBCB

← Older revision		Revision as of 11:29, 9 November 2009
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	Assembly pipelines:		Assembly pipelines:
	# ~/bin/AMOS/minimus3:		# minimus2
			## ~/bin/AMOS/minimus2:
			## Align velvet contigs to one another => direct overlaps
			## Run tigger, make-consensus ...
			# minimus3
			## ~/bin/AMOS/minimus3:
	## Align velvet contigs to one another => direct overlaps		## Align velvet contigs to one another => direct overlaps
	## Align velvet contigs to all complete reference genomes; find contigs that overlap same reference regions => indirect overlaps		## Align velvet contigs to all complete reference genomes; find contigs that overlap same reference regions => indirect overlaps
	## Merge direct & indirect overlaps		## Merge direct & indirect overlaps
	## Run tigger, make-consensus		## Run tigger, make-consensus
	~~# ~/bin/AMOS/AMOScmp-shortReads~~
	~~## Align reads to the "closest" best assembled HPKX reference using soap~~
	~~## Get overlaps~~
	~~## Run casm-layout, make-consensus~~

	nl assembly ctgs min q1 q2 q3 max mean n50 sum		nl assembly ctgs min q1 q2 q3 max mean n50 sum
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	'''AMOScmp''' contigs 100bp+ stats:		'''AMOScmp''' contigs 100bp+ stats:
			Pipeline: AMOScmp-shortReads
			# ~/bin/AMOS/AMOScmp-shortReads
			## Align reads to the "closest" best assembled HPKX reference using soap
			## Get overlaps
			## Run casm-layout, make-consensus

	nl assembly ctgs min q1 q2 q3 max mean n50 sum reads qual ref		nl assembly ctgs min q1 q2 q3 max mean n50 sum reads qual ref
	2 HPKX_1039_AG0C2 286 100 341 2402 8354 90182 5718 12867 1635626 4.7M q00 HPKX_1039_AG4C2		2 HPKX_1039_AG0C2 286 100 341 2402 8354 90182 5718 12867 1635626 4.7M q00 HPKX_1039_AG4C2