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

@@ Line 54: / Line 54: @@
 |}
-http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment
+*http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment
+*[http://lh3lh3.users.sourceforge.net/NGSalign.shtml (NGS toos)]
-[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://main.g2.bx.psu.edu/ galaxy web-page(NGS tools)]
+*[http://en.wikipedia.org/wiki/List_of_alignment_visualization_software List of alignment visualization software]
+*Conversion among formats [http://maq.sourceforge.net/fq_all2std.pl fa_all2std.pl]
-[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html fastx-toolkit]
+*Inverted repeat finder [http://tandem.bu.edu/irf/irf.unix.help.html IRF help] [http://tandem.bu.edu/irf/irf305.macos.download.html download]
-[http://en.wikipedia.org/wiki/List_of_alignment_visualization_software List of alignment visualization software]