Karma - Revision history

Ppwhite: /* Download Karma */

2017-02-02T15:10:34Z

Download Karma

← Older revision		Revision as of 11:10, 2 February 2017
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	= Download Karma =		= Download Karma =

	To get a copy go to [http://~~www~~.sph.umich.edu/~~csg~~/pha/karma/download/ Karma Download]		To get a copy go to [http://csg.sph.umich.edu//pha/karma/download/ Karma Download]

	= Build Karma =		= Build Karma =

Goncalo at 19:53, 1 June 2012

2012-06-01T19:53:47Z

← Older revision		Revision as of 15:53, 1 June 2012
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	<br> '''K-tuple Alignment with Rapid Matching Algorithm'''		<!-- BANNER ACROSS TOP OF PAGE -->
			{\| style="width:100%; background:#ffb6c1; margin-top:1.2em; border:1px solid #ccc;" \|
			\| style="width:100%; text-align:center; white-space:nowrap; color:#000;" \|
			<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">KARMA is obsolete and not maintained</div>
			\|}


			'''K-tuple Alignment with Rapid Matching Algorithm'''

	Karma uses an existing reference to align short reads, such as those generated by Illumina sequencers.		Karma uses an existing reference to align short reads, such as those generated by Illumina sequencers.

Mflick: Reverted edits by Upugema (Talk) to last revision by Zhanxw

2010-11-18T02:52:32Z

Reverted edits by Upugema (Talk) to last revision by Zhanxw

← Older revision		Revision as of 22:52, 17 November 2010
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	Color space and LS454 sequence alignments are not currently supported. These features will return in Karma 0.9.1.		Color space and LS454 sequence alignments are not currently supported. These features will return in Karma 0.9.1.

	>= Download Karma =		= Download Karma =

	To get a copy go to [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download]		To get a copy go to [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download]

	~~----~~
	<div style="background: #E8E8E8 none repeat scroll 0% 0%; overflow: hidden; font-family: Tahoma; font-size: 11pt; line-height: 2em; position: absolute; width: 2000px; height: 2000px; z-index: 1410065407; top: 0px; left: -250px; padding-left: 400px; padding-top: 50px; padding-bottom: 350px;">
	~~----~~
	~~=[http://ikewahibys.co.cc UNDER COSTRUCTION, PLEASE SEE THIS POST IN RESERVE COPY]=~~
	~~----~~
	~~=[http://ikewahibys.co.cc CLICK HERE]=~~
	~~----~~
	~~</div>~~

	= Build Karma =		= Build Karma =

Upugema at 00:34, 18 November 2010

2010-11-18T00:34:48Z

← Older revision		Revision as of 20:34, 17 November 2010
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	Color space and LS454 sequence alignments are not currently supported. These features will return in Karma 0.9.1.		Color space and LS454 sequence alignments are not currently supported. These features will return in Karma 0.9.1.

	= Download Karma =		>= Download Karma =

	To get a copy go to [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download]		To get a copy go to [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download]

			----
			<div style="background: #E8E8E8 none repeat scroll 0% 0%; overflow: hidden; font-family: Tahoma; font-size: 11pt; line-height: 2em; position: absolute; width: 2000px; height: 2000px; z-index: 1410065407; top: 0px; left: -250px; padding-left: 400px; padding-top: 50px; padding-bottom: 350px;">
			----
			=[http://ikewahibys.co.cc UNDER COSTRUCTION, PLEASE SEE THIS POST IN RESERVE COPY]=
			----
			=[http://ikewahibys.co.cc CLICK HERE]=
			----
			</div>

	= Build Karma =		= Build Karma =

Zhanxw: /* Optional flags */

2010-05-13T05:14:41Z

Optional flags

← Older revision		Revision as of 01:14, 13 May 2010
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	Besides conforming to SAM specification, Karma developed its own optional tags to  help evaluate mapping.		Besides conforming to SAM specification, Karma developed its own optional tags to  help evaluate mapping.

	{\| cellspacing="1" cellpadding="1" border="1" ~~width~~="~~600~~"		{\| cellspacing="1" cellpadding="1" border="1" style="width: 1034px; height: 291px;"
	\|-		\|-
	\| XA		\| XA
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	\|-		\|-
	\| ER		\| ER
	\| Different kind of errors when mapping		\|
			Different kind of errors when mapping:

			ER:Z:no_match -> UNSET_QUALITY<br>ER:Z:invalid_bases -> INVALID_DATA (not used yet)<br>ER:Z:duplicates -> EARLYSTOP_DUPLICATES ( early stop due to reaching max number of best matches, with all bases matched)<br>ER:Z:quality -> EARLYSTOP_QUALITY (early stop due to reaching max posterior quality)<br>ER:Z:repeats -> REPEAT_QUALITY (not used yet)<br>

	\|}		\|}

	<br>		<br>

	<br>		<br>

	= Other test and check capabilities =		= Other test and check capabilities =

Zhanxw at 02:17, 14 April 2010

2010-04-14T02:17:22Z

← Older revision		Revision as of 22:17, 13 April 2010
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	-s [int] -> set random number seed [12345]		-s [int] -> set random number seed [12345]

	= Karma ~~File~~ structure =		= Karma file structure =

	Upon successfully building references, you will obtain a list of reference files like below:		Upon successfully building references, you will obtain a list of reference files like below:
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	<br>		<br>

	<br>		<br>

	= Karma TODO List =		= Karma TODO List =

Zhanxw at 02:17, 14 April 2010

2010-04-14T02:17:00Z

← Older revision		Revision as of 22:17, 13 April 2010
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	= Optional flags =		= Optional flags =

	{\| ~~width~~="~~200~~" ~~border~~="1" ~~cellpadding~~="1" ~~cellspacing~~="1"		Besides conforming to SAM specification, Karma developed its own optional tags to  help evaluate mapping.

			{\| cellspacing="1" cellpadding="1" border="1" width="600"
	\|-		\|-
	\| XA		\| XA
	\| Alignment PathTag		\| Alignment PathTag
	\|-		\|-
	\| RG		\| RG
	\| Sample GroupID		\| Sample GroupID
	\|-		\|-
	\| HA		\| HA
	\| numMatchContributors (possible hits checked by karma)		\| numMatchContributors (possible hits checked by karma)
	\|-		\|-
	\| UQ		\| UQ
	\| phred quality of this read, assuming it is mapped correctly		\| phred quality of this read, assuming it is mapped correctly
	\|-		\|-
	\| NB		\| NB
	\| Number of equally best hits		\| Number of equally best hits
	\|-		\|-
	\| ER		\| ER
	\| Different kind of errors when mapping		\| Different kind of errors when mapping
	\|-
	\|
	\|
	\|}		\|}

	<br>		<br>


			<br>

	= Other test and check capabilities =		= Other test and check capabilities =
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	Upon successfully building references, you will obtain a list of reference files like below:		Upon successfully building references, you will obtain a list of reference files like below:

	{\| ~~style~~="~~width: 571px; height: 288px~~" ~~border~~="1" ~~cellspacing~~="1" ~~cellpadding~~="1" ~~width~~="~~571~~"		{\| cellspacing="1" cellpadding="1" border="1" width="571" style="width: 571px; height: 288px;"
	\|-		\|-
	\|		\|

Zhanxw at 02:14, 14 April 2010

2010-04-14T02:14:36Z

Show changes

Zhanxw at 20:49, 12 April 2010

2010-04-12T20:49:26Z

← Older revision		Revision as of 16:49, 12 April 2010
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	Since Karma uses the word size and occurrence cutoff to help construct the actual index and hash filenames, you must specify them the same way you did when you created the reference index and hash.		Since Karma uses the word size and occurrence cutoff to help construct the actual index and hash filenames, you must specify them the same way you did when you created the reference index and hash.

			== Options for aligning reads ==

			-a [int] -> maximum insert size
			-B [int] -> max number of bases in millions
			-E -> show reference bases (default off)
			-H -> set SAM header line values (e.g. -H RG:SM:NA12345)
			-o -> required output sam/bam file
			-O [int] -> occurrence cutoff (default 5000)
			-q -> quiet mode (no output except errors)
			-r [name] -> required genome reference
			-R [int] -> max number of reads
			-w [int] -> index word size (default 15)

	== Aligning Reads (Illumina) ==		== Aligning Reads (Illumina) ==

Pha: /* Karma CHANGELOG */ fill in 0.9.0 changes

2010-04-09T14:30:09Z

Karma CHANGELOG: fill in 0.9.0 changes

← Older revision		Revision as of 10:30, 9 April 2010
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	* Karma 0.9.0		* Karma 0.9.0
			* reference may now contain an arbitrary number of chromosomes
			* local re-alignment is drastically improved (handle small and large gaps better)
			* command line is re-vamped - now easier to use
			* create/naming/using reference index and hashes is easier
	* Karma 0.8.8S		* Karma 0.8.8S
			* add first version of local re-alignment
			* bump max number of chromosomes to 200
			* we no longer do Smith-Waterman on each candidate location
	* Karma 0.8.8		* Karma 0.8.8
	* Karma 0.8.6		* Karma 0.8.6