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Home modified by Abhishek Biswas

Abhishek Biswas — Thu, 17 Sep 2015 15:32:43 -0000

--- v15
+++ v16
@@ -1,6 +1,6 @@
 ## Welcome to your ISQuest wiki! ##

-This file is the user manual for ISQuest version 1.0.
+This file is the user manual for ISQuest version 1.4.1

 ### 1. Building ISQuest Executable ###

@@ -24,6 +24,12 @@
         * Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
         * Download "nt" database and setup as instructed in step(c).
         * Edit PATH environment variable to include the path to isq executable file.
+    3. Installation with MPI
+       * mpic++ should be in PATH.
+       * Run make as usual. A new executable named mpiblast will be built.
+       * Path to mpiblast must be available in the config file as MPIBLAST. This it to make sure this can be invoked from SGE.
+       * Set MPIHOSTCOUNT can be set. Default is 4. 
+       * Run isq as "qsub -pe <env> 1 isq ...."

 ### 3. User Instructions ###

@@ -35,12 +41,14 @@
        BLASTDB=<<SOME PATH="">>\blastdb\
        LOOPCOUNTER=5
        USEPREVBLAST=1
+        MPIBLAST=/scratch/abisw001/ISQuest/isquest-code/
+       MPIHOSTCOUNT=8
     2. A set of contigs in fasta format.
     3. The set of reads used to assemble the contigs in fasta format.
     4. Prefix of the name of the output files.

 The command to execute the file is as follows:
-        >isq <paramter file=""> <contig file=""> <read file=""> output_name_prefix_string
+        >isq <paramter file=""> <contig file="">  <read file=""> output_name_prefix_string

 ### 4. Important Issues  ###
     * The software during the first run will download a lot of GenBank files in GENBANKPATH from NCBI. This will make this run very slow. Future runs will be faster.

Home modified by Abhishek Biswas

Abhishek Biswas — Tue, 21 Jul 2015 17:13:29 -0000

--- v14
+++ v15
@@ -33,7 +33,7 @@
            GENBANKPATH=<<SOME PATH="">>
        BLASTPATH=<SOME PATH="">\blast-2.2.29\bin\
        BLASTDB=<<SOME PATH="">>\blastdb\
-       LOOPCOUNTER=2
+       LOOPCOUNTER=5
        USEPREVBLAST=1
     2. A set of contigs in fasta format.
     3. The set of reads used to assemble the contigs in fasta format.
@@ -51,9 +51,9 @@
 The major output files are:

     * Bunch of *.sam alignment files with corresponding fasta files with same name containing the rference sequence 
-        1. You can import them into Geneious
-        2. Naming Convention <strain_name>_<loopID>_transposaseHit_<level 1="" ID="">_<level 2="" ID="">.*.sam
-    * IS_Contig_Map.txt provides the contig ID and the coordinates of the original transposase hits. 
+        1. You can import them into a viewer tool.
+        2. Naming Convention <strain_name>_<loopID>_transposaseHit_<levelIDs>.*.sam
+    * IS_Contig_Map.txt provides the contig and the coordinates of the original transposase hits. 

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Home modified by Abhishek Biswas

Abhishek Biswas — Tue, 21 Jul 2015 17:11:19 -0000

--- v13
+++ v14
@@ -20,12 +20,12 @@
         * Edit PATH environment variable to include the path to isq executable file.

     2. Installation on Linux
-        a. ISQuest executable file generated in step 1. 
-        b. Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
-        c. Download "nt" database and setup as instructed in step(c).
-        d. Edit PATH environment variable to include the path to isq executable file.
+        * ISQuest executable file generated in step 1. 
+        * Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
+        * Download "nt" database and setup as instructed in step(c).
+        * Edit PATH environment variable to include the path to isq executable file.

-3. User Instructions
+### 3. User Instructions ###

 To use the software you will need:

@@ -40,15 +40,14 @@
     4. Prefix of the name of the output files.

 The command to execute the file is as follows:
+        >isq <paramter file=""> <contig file=""> <read file=""> output_name_prefix_string

-   >isq <paramter file=""> <contig file=""> <read file=""> strain_name
-   
-4. Important points to note:
+### 4. Important Issues  ###
     * The software during the first run will download a lot of GenBank files in GENBANKPATH from NCBI. This will make this run very slow. Future runs will be faster. 
     * The software will do a BLAST search during the first run. This will make the first run slow.       Future runs can use the same BLAST results. If you want to generate new BLAST search use USEPREVBLAST=0
     * The GBFP parser that I am using right now cannot handle certain GenBank file types. There is no support for this anymore and I have to go in and fix the bugs. This will be done in the next release. 

-5. Output
+### 5. Output ###
 The major output files are:

     * Bunch of *.sam alignment files with corresponding fasta files with same name containing the rference sequence 
@@ -56,19 +55,5 @@
         2. Naming Convention <strain_name>_<loopID>_transposaseHit_<level 1="" ID="">_<level 2="" ID="">.*.sam
     * IS_Contig_Map.txt provides the contig ID and the coordinates of the original transposase hits. 

-6. Example usage
-
-Please go to the directory <some_path>\324-958
-
-You will need:
-
-    1. A parameter file "param.conf"
-    2. A set of contigs for 324-958 strain - Contigs324-958.fasta
-    3. The reads - 324-958_A_GGACTCCT-GTAAGGAG_L001_R_TRIM_PAIRED.fasta
-
-Try to execute the following command from command line:
- 
-isq param.conf Contigs324-958.fasta 324-958_A_GGACTCCT-GTAAGGAG_L001_R_TRIM_PAIRED.fasta 324-958
-
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Home modified by Abhishek Biswas

Abhishek Biswas — Tue, 21 Jul 2015 17:06:36 -0000

--- v12
+++ v13
@@ -14,11 +14,10 @@

     1. Installation on Windows
         * ISQuest executable file generated in step 1. 
-   * Download and install Microsoft Visual C++ 2010 Redistributable Package (x64)
-       http://www.microsoft.com/en-us/download/confirmation.aspx?id=14632
-   * Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
-   * Download "nt" database and setup as instructed in step(c).
-   * Edit PATH environment variable to include the path to isq executable file.
+        * Download and install Microsoft Visual C++ 2010 Redistributable Package (x64) http://www.microsoft.com/en-us/download/confirmation.aspx?id=14632
+        * Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
+        * Download "nt" database and setup as instructed in step(c).
+        * Edit PATH environment variable to include the path to isq executable file.

     2. Installation on Linux
         a. ISQuest executable file generated in step 1.

Home modified by Abhishek Biswas

Abhishek Biswas — Tue, 21 Jul 2015 17:01:18 -0000

--- v11
+++ v12
@@ -4,19 +4,21 @@

 ### 1. Building ISQuest Executable ###

-make
+1. Download and unzip the code in a directory. 
+2. Change to the directory. 
+3. Execute command: make

 ### 2. Installation ###

 The ISQuest tool requires some local setup of supporting tools and databases. To install the software you will need: 

     1. Installation on Windows
-        a. ISQuest executable file generated in step 1. 
-   b. Download and install Microsoft Visual C++ 2010 Redistributable Package (x64)
+        * ISQuest executable file generated in step 1. 
+   * Download and install Microsoft Visual C++ 2010 Redistributable Package (x64)
        http://www.microsoft.com/en-us/download/confirmation.aspx?id=14632
-   c. Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
-   d. Download "nt" database and setup as instructed in step(c).
-   e. Edit PATH environment variable to include the path to isq executable file.
+   * Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
+   * Download "nt" database and setup as instructed in step(c).
+   * Edit PATH environment variable to include the path to isq executable file.

     2. Installation on Linux
         a. ISQuest executable file generated in step 1.

Home modified by Abhishek Biswas

Abhishek Biswas — Tue, 21 Jul 2015 16:58:44 -0000

--- v10
+++ v11
@@ -1,12 +1,12 @@
-Welcome to your ISQuest wiki!
+## Welcome to your ISQuest wiki! ##

-This file is the user manual for ISQuest_1.0...
+This file is the user manual for ISQuest version 1.0.

-1. Building ISQuest Executable
+### 1. Building ISQuest Executable ###

 make

-2. Installation
+### 2. Installation ###

 The ISQuest tool requires some local setup of supporting tools and databases. To install the software you will need:

Home modified by Abhishek Biswas

Abhishek Biswas — Tue, 21 Jul 2015 16:54:15 -0000

--- v9
+++ v10
@@ -6,7 +6,7 @@

 make

-+ Installation
+2. Installation

 The ISQuest tool requires some local setup of supporting tools and databases. To install the software you will need: 

@@ -18,13 +18,13 @@
    d. Download "nt" database and setup as instructed in step(c).
    e. Edit PATH environment variable to include the path to isq executable file.

-    + Installation on Linux
+    2. Installation on Linux
         a. ISQuest executable file generated in step 1. 
         b. Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
         c. Download "nt" database and setup as instructed in step(c).
         d. Edit PATH environment variable to include the path to isq executable file.

-* User Instructions
+3. User Instructions

 To use the software you will need:

@@ -34,9 +34,9 @@
        BLASTDB=<<SOME PATH="">>\blastdb\
        LOOPCOUNTER=2
        USEPREVBLAST=1
-    + A set of contigs in fasta format.
-    + The set of reads used to assemble the contigs in fasta format.
-    + Prefix of the name of the output files.
+    2. A set of contigs in fasta format.
+    3. The set of reads used to assemble the contigs in fasta format.
+    4. Prefix of the name of the output files.

 The command to execute the file is as follows:

Home modified by Abhishek Biswas

Abhishek Biswas — Tue, 21 Jul 2015 16:52:11 -0000

--- v8
+++ v9
@@ -6,77 +6,66 @@

 make

-2. Installation
++ Installation

-The ISQuest tool requires some local setup of supporting tools and
-databases.   
+The ISQuest tool requires some local setup of supporting tools and databases. To install the software you will need: 

-2a. Installation on Windows
-
-To install the software you will need: 
-
-   a. ISQuest executable file generated in step 1. 
+    1. Installation on Windows
+        a. ISQuest executable file generated in step 1. 
    b. Download and install Microsoft Visual C++ 2010 Redistributable Package (x64)
        http://www.microsoft.com/en-us/download/confirmation.aspx?id=14632
-   c. Install standalone BLAST. See manual 
-       http://www.ncbi.nlm.nih.gov/books/NBK52637/
+   c. Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
    d. Download "nt" database and setup as instructed in step(c).
    e. Edit PATH environment variable to include the path to isq executable file.

-2b. Installation on Linux
+    + Installation on Linux
+        a. ISQuest executable file generated in step 1. 
+        b. Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
+        c. Download "nt" database and setup as instructed in step(c).
+        d. Edit PATH environment variable to include the path to isq executable file.

-    a. ISQuest executable file generated in step 1. 
-    b. Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
-    c. Download "nt" database and setup as instructed in step(c).
-    d. Edit PATH environment variable to include the path to isq executable file.
-
-3. User Instructions
+* User Instructions

 To use the software you will need:

-   a. Parameter file with the following fields:
-       GENBANKPATH=<<SOME PATH="">>
+    1. Parameter file with the following fields:
+           GENBANKPATH=<<SOME PATH="">>
        BLASTPATH=<SOME PATH="">\blast-2.2.29\bin\
        BLASTDB=<<SOME PATH="">>\blastdb\
        LOOPCOUNTER=2
        USEPREVBLAST=1
-   b. A set of contigs in fasta format.
-   c. The set of reads used to assemble the contigs in fasta format.
-   d. Prefix of the name of the output files.
+    + A set of contigs in fasta format.
+    + The set of reads used to assemble the contigs in fasta format.
+    + Prefix of the name of the output files.

 The command to execute the file is as follows:

    >isq <paramter file=""> <contig file=""> <read file=""> strain_name

-Important points to note:
-   a. The software during the first run will download a lot of GenBank files in GENBANKPATH from NCBI. 
-      This will make this run very slow. Future runs will be faster. 
-   b. The software will do a BLAST search during the first run. This will make the first run slow. 
-       Future runs can use the same BLAST results. If you want to generate new BLAST search use 
-      USEPREVBLAST=0
-   c. The GBFP parser that I am using right now cannot handle certain GenBank file types. 
-      There is no support for this anymore nad I hace to go in and fix the bugs.
-      This will be done in the next release. 
+4. Important points to note:
+    * The software during the first run will download a lot of GenBank files in GENBANKPATH from NCBI. This will make this run very slow. Future runs will be faster. 
+    * The software will do a BLAST search during the first run. This will make the first run slow.       Future runs can use the same BLAST results. If you want to generate new BLAST search use USEPREVBLAST=0
+    * The GBFP parser that I am using right now cannot handle certain GenBank file types. There is no support for this anymore and I have to go in and fix the bugs. This will be done in the next release. 

-
+5. Output
 The major output files are:

-   a. Bunch of *.sam alignment files with corresponding fasta files with same name containing the reference sequence 
-       i. You can import them into Geneious
-       ii. Naming Convention <strain_name>_<loopID>_transposaseHit_<level 1="" ID="">_<level 2="" ID="">.*.sam
-   b. IS_Contig_Map.txt provides the contig ID and the coordinates of the original transposase hits. 
+    * Bunch of *.sam alignment files with corresponding fasta files with same name containing the rference sequence 
+        1. You can import them into Geneious
+        2. Naming Convention <strain_name>_<loopID>_transposaseHit_<level 1="" ID="">_<level 2="" ID="">.*.sam
+    * IS_Contig_Map.txt provides the contig ID and the coordinates of the original transposase hits. 

-4. Example usage
+6. Example usage

-Please go to the directory D:\gauthier\MarinumStrains\324-958
+Please go to the directory <some_path>\324-958

-You will find:
+You will need:

-1. A parameter file "param.conf"
-2. A set of contigs for 324-958 strain - Contigs324-958.fasta
-3. The reads - 324-958_A_GGACTCCT-GTAAGGAG_L001_R_TRIM_PAIRED.fasta
+    1. A parameter file "param.conf"
+    2. A set of contigs for 324-958 strain - Contigs324-958.fasta
+    3. The reads - 324-958_A_GGACTCCT-GTAAGGAG_L001_R_TRIM_PAIRED.fasta

-Try to execute the following command from commandline:
+Try to execute the following command from command line:

 isq param.conf Contigs324-958.fasta 324-958_A_GGACTCCT-GTAAGGAG_L001_R_TRIM_PAIRED.fasta 324-958

Home modified by Abhishek Biswas

Abhishek Biswas — Tue, 21 Jul 2015 16:43:04 -0000

--- v7
+++ v8
@@ -23,20 +23,41 @@
    d. Download "nt" database and setup as instructed in step(c).
    e. Edit PATH environment variable to include the path to isq executable file.

+2b. Installation on Linux
+
+    a. ISQuest executable file generated in step 1. 
+    b. Install standalone BLAST. See manual http://www.ncbi.nlm.nih.gov/books/NBK52637/
+    c. Download "nt" database and setup as instructed in step(c).
+    d. Edit PATH environment variable to include the path to isq executable file.
+
 3. User Instructions

 To use the software you will need:

-   a. Parameter file with three fields:
+   a. Parameter file with the following fields:
+       GENBANKPATH=<<SOME PATH="">>
        BLASTPATH=<SOME PATH="">\blast-2.2.29\bin\
        BLASTDB=<<SOME PATH="">>\blastdb\
        LOOPCOUNTER=2
-   b. A set of contigs in fasta format
-   c. The set of reads used to assemble the contigs in fasta format
+       USEPREVBLAST=1
+   b. A set of contigs in fasta format.
+   c. The set of reads used to assemble the contigs in fasta format.
+   d. Prefix of the name of the output files.

 The command to execute the file is as follows:

    >isq <paramter file=""> <contig file=""> <read file=""> strain_name
+   
+Important points to note:
+   a. The software during the first run will download a lot of GenBank files in GENBANKPATH from NCBI. 
+      This will make this run very slow. Future runs will be faster. 
+   b. The software will do a BLAST search during the first run. This will make the first run slow. 
+       Future runs can use the same BLAST results. If you want to generate new BLAST search use 
+      USEPREVBLAST=0
+   c. The GBFP parser that I am using right now cannot handle certain GenBank file types. 
+      There is no support for this anymore nad I hace to go in and fix the bugs.
+      This will be done in the next release. 
+

 The major output files are:

Home modified by Abhishek Biswas

Abhishek Biswas — Mon, 06 Jul 2015 07:40:33 -0000

--- v6
+++ v7
@@ -8,7 +8,7 @@

 2. Installation

-The ISQuest tool requires dome local setup of supporting tools and
+The ISQuest tool requires some local setup of supporting tools and
 databases.   

 2a. Installation on Windows