Recent changes to Home

WikiPage Home modified by Rebecca Sealfon

Rebecca Sealfon — Thu, 04 Aug 2011 17:41:12 -0000

--- v2 
+++ v3 
@@ -1,19 +1,0 @@
-About:
-
-MARSHAL enables short-read nucleotide alignment software to utilize multiple references. It allows the end-user to choose which aligner is used, since it works by preprocessing the alignment input and postprocessing the alignment output. It is most effective when run with a set of references that are relatively similar to one another and to the reads, but are polymorphic with respect to specific long insertions and deletions (indels).
-
-The program accepts input of one or more short read files, a FASTA primary reference, a tab-delimited file with a formatted list of long indels, and FASTA sequence files containing the insertions. An optional preprocessing step identifies the indels from pairwise or multiple-sequence alignment between the primary reference and other reference(s). Prior to short-read alignment, the indel information is used to create an initial chimeric reference. This chimera is inclusive of the primary reference and all the insertions, and is designed to enable the short-read aligner to adequately map the reads to the indels. After the aligner is run, the coverage of each indel is analyzed and its presence vs. absence evaluated. The end-user may create an optimized chimeric reference containing the combination of indels discovered in the short reads.
-
-The software and algorithm were developed in the Department of Computer Science at Columbia University. They are built with Java and bash and tested in the GNU/Linux environment; the source is distributed here in a .tar.gz package under the GPL license.
-
-
-Usage:
-
-The downloaded file can be uncompressed by typing
-$ tar -zxvf marshal-XXX.tar
-where XXX is the version obtained.
-
-Compile the program in the main download directory with
-$ make all
-
-A tutorial and complete usage information for all scripts are included in the manual.

WikiPage Home modified by Rebecca Sealfon

Rebecca Sealfon — Thu, 04 Aug 2011 17:33:57 -0000

--- v1 
+++ v2 
@@ -1,5 +1,19 @@
-Welcome to your wiki!
-
-This is the default page, edit it as you see fit. To add a page simply reference it within brackets, e.g.: [SamplePage].
-
-The wiki uses [Markdown](/p/marshalbio/home/markdown_syntax/) syntax.
+About:
+
+MARSHAL enables short-read nucleotide alignment software to utilize multiple references. It allows the end-user to choose which aligner is used, since it works by preprocessing the alignment input and postprocessing the alignment output. It is most effective when run with a set of references that are relatively similar to one another and to the reads, but are polymorphic with respect to specific long insertions and deletions (indels).
+
+The program accepts input of one or more short read files, a FASTA primary reference, a tab-delimited file with a formatted list of long indels, and FASTA sequence files containing the insertions. An optional preprocessing step identifies the indels from pairwise or multiple-sequence alignment between the primary reference and other reference(s). Prior to short-read alignment, the indel information is used to create an initial chimeric reference. This chimera is inclusive of the primary reference and all the insertions, and is designed to enable the short-read aligner to adequately map the reads to the indels. After the aligner is run, the coverage of each indel is analyzed and its presence vs. absence evaluated. The end-user may create an optimized chimeric reference containing the combination of indels discovered in the short reads.
+
+The software and algorithm were developed in the Department of Computer Science at Columbia University. They are built with Java and bash and tested in the GNU/Linux environment; the source is distributed here in a .tar.gz package under the GPL license.
+
+
+Usage:
+
+The downloaded file can be uncompressed by typing
+$ tar -zxvf marshal-XXX.tar
+where XXX is the version obtained.
+
+Compile the program in the main download directory with
+$ make all
+
+A tutorial and complete usage information for all scripts are included in the manual.

WikiPage Home modified by Rebecca Sealfon

Rebecca Sealfon — Thu, 04 Aug 2011 13:54:29 -0000

Welcome to your wiki! This is the default page, edit it as you see fit. To add a page simply reference it within brackets, e.g.: [SamplePage]. The wiki uses [Markdown](/p/marshalbio/home/markdown_syntax/) syntax.