Recent changes to OperaMS

OperaMS modified by Denis Bertrand

Denis Bertrand — Tue, 02 Apr 2013 02:13:36 -0000

--- v11
+++ v12
@@ -94,6 +94,7 @@
 References
 ==========
 * OperaMS was developed in the Genome Institute of Singapore and University of Maryland, College Park.
+* OperaMS uses [Opera](https://sourceforge.net/p/operasf/wiki/The%20Opera%20wiki/) to produce the scaffolds. 
 * Contacts: 
     * bertrandd@gis.a-star.edu.sg (Denis Bertrand)
     * smuthiah@umiacs.umd.edu (M. Senthil Kumar)

WikiPage OperaMS modified by Senthil

Senthil — Thu, 28 Mar 2013 15:31:08 -0000

--- v10
+++ v11
@@ -55,14 +55,14 @@

 -------------

-Format of Configuration File
+Format of the Configuration File
 ===========

 1. **CONTIGS** full path to your contigs file in *.fasta* format.

 + **COVERAGEBAM** mapping file used to estimate the contig coverage (we recommend using the *.bam* mapping file of highest coverage).

-+ **LIB** full path to the mapping file specifying the location of paired-end reads on the contigs (input to *OperaMS*; see bin/preprocess_reads.pl). 
++ **LIB** full path to the mapping file specifying the location of paired-end reads on the contigs (input to *OperaMS*; see bin/preprocess_reads.pl). If you have multiple libraries, they can be entered using the same format in different lines. 

 + **EDGE_BUNDLESIZE_THRESHOLD** Scaffold edges that are supported by less than this number of paired-reads are discarded as noise. By default, we require *>= 5* paired-reads to consider an edge as valid.

WikiPage OperaMS modified by Senthil

Senthil — Thu, 28 Mar 2013 15:29:45 -0000

--- v9
+++ v10
@@ -36,7 +36,7 @@
     perl bin/preprocess_reads.pl   
      ()

-where mapping-tool should be either bwa or bowtie (default) and read-file-1 and read-file-2 contain paired-end reads in fasta or fastq format. Note that all assembled sequences should be provided in this step to ensure that reads are correctly mapped. Opera has a "contig_size_threshold" parameter to allow users to filter small contigs (default value of 500bp) during the scaffolding step.
+where mapping-tool is either bowtie(default) or bwa, and read-file-1 and read-file-2 contain paired-end reads in fasta or fastq format. Note that all assembled sequences should be provided in this step to ensure that reads are correctly mapped. Opera has a "contig_size_threshold" parameter to allow users to filter small contigs (default value of 500bp) during the scaffolding step.
 Note that the binaries "samtools", "bwa", "bowtie" and "bowtie-build" are assumed to be in the path. If not, the third line of preprocess_reads.pl should be edited appropriately.

 2.Provide parameters to OperaMS
@@ -64,19 +64,19 @@

 + **LIB** full path to the mapping file specifying the location of paired-end reads on the contigs (input to *OperaMS*; see bin/preprocess_reads.pl). 

-+ **EDGE_BUNDLESIZE_THRESHOLD** Scaffold edges that are supported by less than this number of paired-reads are discarded as noise. By default, we require *>= 5* edges to consider an edge as valid. 
++ **EDGE_BUNDLESIZE_THRESHOLD** Scaffold edges that are supported by less than this number of paired-reads are discarded as noise. By default, we require *>= 5* paired-reads to consider an edge as valid. 

 + **OUTPUTDIR** the directory into which all results are written.

-+ **SAMTOOLS** full path to *samtools* executable.
++ **SAMTOOLS** full path to the *samtools* executable.

 + **APACHECOMMONSMATH** full path to *apache-commons-math3.0.jar*

 + **JVMREQ** JVM memory requirement. Depending on the complexity of the dataset, you might need to reserve more memory for Sigma's graph handling. We have found that *5GB is enough for the variety of large scale datasets we have handled. 

-+ **KMER_SIZE** KMER_SIZE used to perfom the initial contig assembly (using for exemple Velvet or SOAPdenovo).
++ **KMER_SIZE** the KMER_SIZE used to perform the initial contig assembly (using for example, Velvet or SOAPdenovo).

-####Exemple of configuration file:####
+####An Example Configuration File:####

    CONTIGS path/to/contigs.fa
    COVERAGEBAM path/to/lib3.bam    
@@ -93,7 +93,7 @@
 --------------------------
 References
 ==========
-* OperaMS was developed in the Genome Institute of Singapore and University of Maryland, College Park
+* OperaMS was developed in the Genome Institute of Singapore and University of Maryland, College Park.
 * Contacts: 
     * bertrandd@gis.a-star.edu.sg (Denis Bertrand)
     * smuthiah@umiacs.umd.edu (M. Senthil Kumar)

WikiPage OperaMS modified by Denis Bertrand

Denis Bertrand — Thu, 28 Mar 2013 09:42:46 -0000

--- v8
+++ v9
@@ -93,7 +93,7 @@
 --------------------------
 References
 ==========
-* Opera was developed in the Genome Institute of Singapore and University of Maryland, College Park
+* OperaMS was developed in the Genome Institute of Singapore and University of Maryland, College Park
 * Contacts: 
     * bertrandd@gis.a-star.edu.sg (Denis Bertrand)
     * smuthiah@umiacs.umd.edu (M. Senthil Kumar)

WikiPage OperaMS modified by Denis Bertrand

Denis Bertrand — Thu, 28 Mar 2013 09:41:49 -0000

--- v7
+++ v8
@@ -90,6 +90,7 @@
    JVMREQ  5g  #optional
    KMER_SIZE   31

+--------------------------
 References
 ==========
 * Opera was developed in the Genome Institute of Singapore and University of Maryland, College Park

WikiPage OperaMS modified by Denis Bertrand

Denis Bertrand — Thu, 28 Mar 2013 09:41:07 -0000

--- v6
+++ v7
@@ -98,3 +98,5 @@
     * smuthiah@umiacs.umd.edu (M. Senthil Kumar)
 * Sourceforge Admins:
 [[project_admins]]
+
+Please feel free to contact us if you find bugs, have suggestions, need help etc. Use the discussion forum, the mailing-list or simply mail us directly.

WikiPage OperaMS modified by Denis Bertrand

Denis Bertrand — Thu, 28 Mar 2013 09:40:04 -0000

--- v5
+++ v6
@@ -92,6 +92,9 @@

 References
 ==========
-
+* Opera was developed in the Genome Institute of Singapore and University of Maryland, College Park
+* Contacts: 
+    * bertrandd@gis.a-star.edu.sg (Denis Bertrand)
+    * smuthiah@umiacs.umd.edu (M. Senthil Kumar)
 * Sourceforge Admins:
 [[project_admins]]

WikiPage OperaMS modified by Denis Bertrand

Denis Bertrand — Thu, 28 Mar 2013 09:28:40 -0000

--- v4
+++ v5
@@ -85,8 +85,8 @@
    LIB path/to/lib3.bam
    EDGE_BUNDLESIZE_THRESHOLD   5   #optional
    OUTPUTDIR   directory
-   SAMTOOLS    path
-   APACHECOMMONSMATH   path
+   SAMTOOLS    path/to/samtools
+   APACHECOMMONSMATH   path/to/commons-math3-3.0.jar
    JVMREQ  5g  #optional
    KMER_SIZE   31

WikiPage OperaMS modified by Denis Bertrand

Denis Bertrand — Thu, 28 Mar 2013 09:23:01 -0000

--- v3
+++ v4
@@ -37,14 +37,14 @@
      ()

 where mapping-tool should be either bwa or bowtie (default) and read-file-1 and read-file-2 contain paired-end reads in fasta or fastq format. Note that all assembled sequences should be provided in this step to ensure that reads are correctly mapped. Opera has a "contig_size_threshold" parameter to allow users to filter small contigs (default value of 500bp) during the scaffolding step.
-Note that the binaries "bwa", "bowtie" and "bowtie-build" are assumed to be in the path. If not, the third line of preprocess_reads.pl should be edited appropriately.
+Note that the binaries "samtools", "bwa", "bowtie" and "bowtie-build" are assumed to be in the path. If not, the third line of preprocess_reads.pl should be edited appropriately.

 2.Provide parameters to OperaMS

     cd path/to/OperaMS
     perl runOperaMS.pl  

-where the configuration-file provides information on the contig file, mapping files and output directory to use (see below for the format).
+where the configuration-file provides information on the contig file, mapping files and output directory (see below for the format).

 ----------

WikiPage OperaMS modified by Denis Bertrand

Denis Bertrand — Thu, 28 Mar 2013 09:05:12 -0000

--- v2
+++ v3
@@ -32,6 +32,7 @@

 1.Reads need to be mapped onto contigs/scaffolds (currently we provide a script that uses bowtie/bwa to do this):

+    cd path/to/OperaMS
     perl bin/preprocess_reads.pl   
      ()

@@ -41,10 +42,9 @@
 2.Provide parameters to OperaMS

     cd path/to/OperaMS
-    ./runOperaMS.pl  
-     Configuration file
+    perl runOperaMS.pl  

-where the configuration file provides information on the contig file, mapping files and output directory to use (see below for the format).
+where the configuration-file provides information on the contig file, mapping files and output directory to use (see below for the format).

 ----------