Wikiomics:RNA-Seq - Revision history

Darek Kedra: /* last */

Darek Kedra — Fri, 09 Nov 2012 13:35:35 GMT

last

←Older revision		Revision as of 13:35, 9 November 2012
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	www: http://last.cbrc.jp/		www: http://last.cbrc.jp/

-	Latest: last-~~250~~.zip from 2012.08.16	+	Latest: last-262.zip from 2012.10.23

	paper: http://genome.cshlp.org/content/21/3/487.full		paper: http://genome.cshlp.org/content/21/3/487.full

Darek Kedra — Fri, 09 Nov 2012 13:32:05 GMT

HMMSplicer

←Older revision		Revision as of 13:32, 9 November 2012
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	current version: 0.9.5 from 2010.11.25		current version: 0.9.5 from 2010.11.25

-	active development: maybe (no new release in a ~~year~~)	+	active development: maybe (no new release in a 2 years)

	base mapper: bowtie		base mapper: bowtie

Darek Kedra — Fri, 09 Nov 2012 13:31:00 GMT

GEM

←Older revision		Revision as of 13:31, 9 November 2012
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	===GEM===		===GEM===
-	~~http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=The_GEM_library~~

-	current version: GEM-binaries-Linux-x86_64-~~20100419~~-~~003425~~.tbz2	+	web: http://algorithms.cnag.cat/wiki/The_GEM_library
-	active development: yes ~~(personal communication)~~	+
		+	current version: GEM-binaries-Linux-x86_64-core_i3-20121106-022124.tbz2 from 2012-11-06
		+	active development: yes

	base mapper: gem-mapper and gem-split-mapper		base mapper: gem-mapper and gem-split-mapper

	Developed in Ocaml and Python.		Developed in Ocaml and Python.
-	Two step mapping (unspliced mode first, then unmapped reads are mapped with splicing).	+	Two step mapping (unspliced mode first, then unmapped reads are mapped with splicing).

		+	Article: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2221.html

	===HMMSplicer===		===HMMSplicer===

Darek Kedra — Fri, 09 Nov 2012 13:28:11 GMT

GMAP/GSNAP

←Older revision		Revision as of 13:28, 9 November 2012
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	http://research-pub.gene.com/gmap/		http://research-pub.gene.com/gmap/

-	current version: 2012-06-25	+	current version: 2012-11-07

	active developement: yes		active developement: yes

-	FastA and FASTQ input, support for paired ends, gziped fastq files	+	FastA and FASTQ input, support for paired ends, gziped fastq files, circular chromosomes

Darek Kedra — Wed, 12 Sep 2012 14:00:02 GMT

last

←Older revision		Revision as of 14:00, 12 September 2012
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	www: http://last.cbrc.jp/		www: http://last.cbrc.jp/

-	Latest: last-~~230~~.zip ~~relased~~ 2012.06.01	+	Latest: last-250.zip from 2012.08.16

	paper: http://genome.cshlp.org/content/21/3/487.full		paper: http://genome.cshlp.org/content/21/3/487.full

Darek Kedra — Wed, 12 Sep 2012 13:44:31 GMT

Spliced Mappers (in developement)

←Older revision		Revision as of 13:44, 12 September 2012
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	==Spliced Mappers (in developement)==		==Spliced Mappers (in developement)==

-	===~~PALMapper (fusion of GenomeMapper & QPALMA)~~===	+	=== Olego ===
		+	web: http://ngs-olego.sourceforge.net/

		+
		+
		+	===PALMapper (fusion of GenomeMapper & QPALMA)===

	web: http://raetschlab.org//suppl/palmapper		web: http://raetschlab.org//suppl/palmapper
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	Transcriptome Assembly Utility: requires already mapped input.		Transcriptome Assembly Utility: requires already mapped input.
	Compatible mappers: Blat, Eland and HashMatch. Also accepts gff3 files.		Compatible mappers: Blat, Eland and HashMatch. Also accepts gff3 files.
-
-
-

	==Not spliced==		==Not spliced==

Darek Kedra — Mon, 03 Sep 2012 19:29:57 GMT

GMAP/GSNAP

←Older revision		Revision as of 19:29, 3 September 2012
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	FastA and FASTQ input, support for paired ends, gziped fastq files		FastA and FASTQ input, support for paired ends, gziped fastq files

		+
		+	To compile:
		+	<pre>
		+
		+	./configure --prefix=/some/path/for_install/ --with-gmapdb=/path_to/gmap_DBs/ --with-samtools=/path_to/samtools_0.1.18/
		+	make
		+	make install
		+	</pre>
		+
		+	To run:
	<pre>		<pre>
	gsnap --dir=genome_directory --db=genome_database --batch=2 --localsplicedist=10000 --nthreads=4 --nofails my_reads.fasta		gsnap --dir=genome_directory --db=genome_database --batch=2 --localsplicedist=10000 --nthreads=4 --nofails my_reads.fasta

Darek Kedra — Mon, 02 Jul 2012 14:42:45 GMT

GMAP/GSNAP

←Older revision		Revision as of 14:42, 2 July 2012
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	http://research-pub.gene.com/gmap/		http://research-pub.gene.com/gmap/

-	current version: 2012-06-02	+	current version: 2012-06-25

	active developement: yes		active developement: yes

Darek Kedra — Mon, 02 Jul 2012 14:42:04 GMT

Tophat and Cufflinks

←Older revision		Revision as of 14:42, 2 July 2012
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	web: http://cufflinks.cbcb.umd.edu/		web: http://cufflinks.cbcb.umd.edu/

-	current version: 2.0.0 released 2012.05.~~04 (New!)~~	+	current version: 2.0.1 released 2012.06.15

	===GMAP/GSNAP===		===GMAP/GSNAP===

Darek Kedra — Mon, 02 Jul 2012 14:41:13 GMT

Spliced Mappers (tested)