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Revision as of 17:37, 12 June 2010 (view source) Igchoi (Talk | contribs) (→Abyss) ← Older edit		Revision as of 09:07, 29 July 2011 (view source) Gnusnah (Talk | contribs) Newer edit →
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-	==Softwares==	+	=Softwares=
-	===Abyss===	+	{| class="wikitable" style="text-align:center" border="1"
-	*Features: 1) parallel assembly	+	|+
-	*Download from this [http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.2.0 link] - release 1.2.0 (June 2010)	+	|-
-	*Solving an [http://groups.google.com/group/abyss-users/browse_thread/thread/6b8710a65ec4a691 installation error]	+	|Software || Version || Input || Output || Location(machine/folder)
		+	|-
		+	|[[Newbler]] || 2.3(091027_1459) || || || panflam,panpyro
		+	|-
		+	|Phrap || 0.990329([[Phrap0.990329_patch]]) || ||  || panflam
		+	|-
		+	|Phrap || 1.090518 || ||  || panflam
		+	|-
		+	|Consed || 090206 || ||  || panflam
		+	|-
		+	|CABOG(celera) || 6.1 || sanger, 454(.sff), illumina(fastq), fastq || [[CABOG_output]] || panflam,panpyro
		+	|-
		+	|maq || 0.7.1 || ref:fasta, read:illumina, long read(not good) ||  || panflam,panpyro
		+	|-
		+	|abyss [[http://seqanswers.com/wiki/ABySS]] || 1.2.0 || 454, illumina ||  || panflam
		+	|-
		+	|SOAPdenovo || 1.04 || illumina ||  ||  panflam
		+	|-
		+	|SOAPaligner ||  || illumina ||  ||  panflam
		+	|-
		+	|Corrector(soap package) || 1.00 || fasta,fastq || || panflam
		+	|-
		+	|GapCloser(soap package) || 1.10 || fasta,fastq || || panflam
		+	|-
		+	|MIRA || || sanger,454,illumina ||  ||
		+	|-
		+	|gapResolution || || newbler results || fasta,qual ||
		+	|-
		+	|Dupfinisher || || ace file || ||
		+	|-
		+	|AutoEditor || 1.20 || .contig(TIGR) || ||
		+	|-
		+	|[http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=rnammer rnammer] || 1.2 || fasta || gff2 || panflam
		+	|-
		+	|hmmer || 2.3.2(for rnammer), 3 || || || panflam.panpyro
		+	|-
		+	|tRNAscan-SE || 1.23|| || ||panflam,panpyro
		+	|-
		+	|BlastViewer || || || ||panflam
		+	|-
		+	|M-GCAT || || || ||panflam,panpyro
		+	|-
		+	|bowtie || || illumina || ||
		+	|-
		+	|Velvet || || illumina || ||
		+	|-
		+	|MAQ || || illumina || ||
		+	|-
		+	|Polisher || || illumina || ||
		+	|}
		+
		+	http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment
		+
		+	[http://lh3lh3.users.sourceforge.net/NGSalign.shtml (NGS toos)]
		+
		+	[http://main.g2.bx.psu.edu/ galaxy web-page(NGS tools)]
		+
		+	[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html fastx-toolkit]
		+
		+	[http://en.wikipedia.org/wiki/List_of_alignment_visualization_software List of alignment visualization software]

---

Revision as of 09:07, 29 July 2011

Softwares

Software	Version	Input	Output	Location(machine/folder)
Newbler	2.3(091027_1459)			panflam,panpyro
Phrap	0.990329(Phrap0.990329_patch)			panflam
Phrap	1.090518			panflam
Consed	090206			panflam
CABOG(celera)	6.1	sanger, 454(.sff), illumina(fastq), fastq	CABOG_output	panflam,panpyro
maq	0.7.1	ref:fasta, read:illumina, long read(not good)		panflam,panpyro
abyss [[1]]	1.2.0	454, illumina		panflam
SOAPdenovo	1.04	illumina		panflam
SOAPaligner		illumina		panflam
Corrector(soap package)	1.00	fasta,fastq		panflam
GapCloser(soap package)	1.10	fasta,fastq		panflam
MIRA		sanger,454,illumina
gapResolution		newbler results	fasta,qual
Dupfinisher		ace file
AutoEditor	1.20	.contig(TIGR)
rnammer	1.2	fasta	gff2	panflam
hmmer	2.3.2(for rnammer), 3			panflam.panpyro
tRNAscan-SE	1.23			panflam,panpyro
BlastViewer				panflam
M-GCAT				panflam,panpyro
bowtie		illumina
Velvet		illumina
MAQ		illumina
Polisher		illumina

http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment

(NGS toos)

galaxy web-page(NGS tools)

fastx-toolkit

List of alignment visualization software