Recent changes to Home

Home modified by Solaiappan Manimaran

Solaiappan Manimaran — Sat, 22 Nov 2014 03:18:08 -0000

--- v16
+++ v17
@@ -27,8 +27,8 @@
 Optional:
 ---------
 * If you want to install the complete PathoDB and download the complete NT library with the taxonomy id, you could download it from the following links:
-[ftp://pathoscope.bumc.bu.edu/data/pathodb.sql.gz]
-[ftp://pathoscope.bumc.bu.edu/data/nt_ti.fa.gz]
+<ftp: pathoscope.bumc.bu.edu="" data="" pathodb.sql.gz="">
+<ftp: pathoscope.bumc.bu.edu="" data="" nt_ti.fa.gz="">

 2. Running

Home modified by Solaiappan Manimaran

Solaiappan Manimaran — Sat, 22 Nov 2014 03:12:48 -0000

--- v15
+++ v16
@@ -23,6 +23,12 @@
 + Extract the code to a separate folder
 You could issue the following command to extract the files:
 "tar xvf pathoscope_2.0.tar.gz"
+
+Optional:
+---------
+* If you want to install the complete PathoDB and download the complete NT library with the taxonomy id, you could download it from the following links:
+[ftp://pathoscope.bumc.bu.edu/data/pathodb.sql.gz]
+[ftp://pathoscope.bumc.bu.edu/data/nt_ti.fa.gz]

 2. Running

Home modified by Solaiappan Manimaran

Solaiappan Manimaran — Thu, 20 Nov 2014 05:11:21 -0000

--- v14
+++ v15
@@ -7,9 +7,13 @@
 Pathoscope 2.0 consists of four core and two optional analysis modules for sequencing-based metagenomic profiling. The PathoLib module extracts genome reference libraries (target or host/filter) from all available sequences in the NCBI Nucleotide database that belong to a user-defined taxonomic clade. The PathoMap module aligns the reads to the target reference library and removes any reads that have sequence similarity with the host or filter genomes. PathoID resolves read ambiguity, identifies which of the target genomes are present in the sample and estimates the proportions of reads originating from each genome. PathoReport provides two report files: 1) a summary report (.tsv) that contains the numbers and proportions of reads aligned to each genome identified in the sample, and 2) detailed report (.xml) including read coverage, read assignments, and contiguous sequences generated by combining the reads. The PathoDB is an optional module that provides additional annotation (organism taxonomic lineage, gene loci, protein products) for all sequences identified in the sample. The PathoQC module can be used to preprocess the reads prior to alignment with PathoMap.

 Please refer to the following papers: 
-*  Pathoscope: Species identification and strain attribution with unassembled sequencing data; at http://genome.cshlp.org/content/23/10/1721
+* Pathoscope: Species identification and strain attribution with unassembled sequencing data; at http://genome.cshlp.org/content/23/10/1721

 *  PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples; at http://www.microbiomejournal.com/content/2/1/33
+
+Tutorial:
+http://sourceforge.net/projects/pathoscope/files/pathoscope2.0_v0.02_tutorial.pdf
+

 1. Installation
 ---------------

Home modified by Solaiappan Manimaran

Solaiappan Manimaran — Thu, 20 Nov 2014 05:06:09 -0000

--- v13
+++ v14
@@ -7,9 +7,9 @@
 Pathoscope 2.0 consists of four core and two optional analysis modules for sequencing-based metagenomic profiling. The PathoLib module extracts genome reference libraries (target or host/filter) from all available sequences in the NCBI Nucleotide database that belong to a user-defined taxonomic clade. The PathoMap module aligns the reads to the target reference library and removes any reads that have sequence similarity with the host or filter genomes. PathoID resolves read ambiguity, identifies which of the target genomes are present in the sample and estimates the proportions of reads originating from each genome. PathoReport provides two report files: 1) a summary report (.tsv) that contains the numbers and proportions of reads aligned to each genome identified in the sample, and 2) detailed report (.xml) including read coverage, read assignments, and contiguous sequences generated by combining the reads. The PathoDB is an optional module that provides additional annotation (organism taxonomic lineage, gene loci, protein products) for all sequences identified in the sample. The PathoQC module can be used to preprocess the reads prior to alignment with PathoMap.

 Please refer to the following papers: 
-1. Pathoscope: Species identification and strain attribution with unassembled sequencing data; at http://genome.cshlp.org/content/23/10/1721
+*  Pathoscope: Species identification and strain attribution with unassembled sequencing data; at http://genome.cshlp.org/content/23/10/1721

-+  PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples; at http://www.microbiomejournal.com/content/2/1/33
+*  PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples; at http://www.microbiomejournal.com/content/2/1/33

 1. Installation
 ---------------

Home modified by Solaiappan Manimaran

Solaiappan Manimaran — Thu, 20 Nov 2014 05:04:08 -0000

--- v12
+++ v13
@@ -8,6 +8,7 @@

 Please refer to the following papers: 
 1. Pathoscope: Species identification and strain attribution with unassembled sequencing data; at http://genome.cshlp.org/content/23/10/1721
+
 +  PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples; at http://www.microbiomejournal.com/content/2/1/33

 1. Installation

Home modified by Solaiappan Manimaran

Solaiappan Manimaran — Thu, 20 Nov 2014 05:01:14 -0000

--- v11
+++ v12
@@ -1,14 +1,14 @@
 Pathoscope 2.0
 ==============

-0. Introduction:
-----------------
+Introduction:
+-------------

 Pathoscope 2.0 consists of four core and two optional analysis modules for sequencing-based metagenomic profiling. The PathoLib module extracts genome reference libraries (target or host/filter) from all available sequences in the NCBI Nucleotide database that belong to a user-defined taxonomic clade. The PathoMap module aligns the reads to the target reference library and removes any reads that have sequence similarity with the host or filter genomes. PathoID resolves read ambiguity, identifies which of the target genomes are present in the sample and estimates the proportions of reads originating from each genome. PathoReport provides two report files: 1) a summary report (.tsv) that contains the numbers and proportions of reads aligned to each genome identified in the sample, and 2) detailed report (.xml) including read coverage, read assignments, and contiguous sequences generated by combining the reads. The PathoDB is an optional module that provides additional annotation (organism taxonomic lineage, gene loci, protein products) for all sequences identified in the sample. The PathoQC module can be used to preprocess the reads prior to alignment with PathoMap.

 Please refer to the following papers: 
-1. "Pathoscope: Species identification and strain attribution with unassembled sequencing data" at http://genome.cshlp.org/content/23/10/1721
-+ "PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples" at http://www.microbiomejournal.com/content/2/1/33
+1. Pathoscope: Species identification and strain attribution with unassembled sequencing data; at http://genome.cshlp.org/content/23/10/1721
++  PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples; at http://www.microbiomejournal.com/content/2/1/33

 1. Installation
 ---------------

Home modified by Solaiappan Manimaran

Solaiappan Manimaran — Thu, 20 Nov 2014 04:53:46 -0000

--- v10
+++ v11
@@ -1,15 +1,14 @@
 Pathoscope 2.0
 ==============

-Introduction:
--------------
+0. Introduction:
+----------------

 Pathoscope 2.0 consists of four core and two optional analysis modules for sequencing-based metagenomic profiling. The PathoLib module extracts genome reference libraries (target or host/filter) from all available sequences in the NCBI Nucleotide database that belong to a user-defined taxonomic clade. The PathoMap module aligns the reads to the target reference library and removes any reads that have sequence similarity with the host or filter genomes. PathoID resolves read ambiguity, identifies which of the target genomes are present in the sample and estimates the proportions of reads originating from each genome. PathoReport provides two report files: 1) a summary report (.tsv) that contains the numbers and proportions of reads aligned to each genome identified in the sample, and 2) detailed report (.xml) including read coverage, read assignments, and contiguous sequences generated by combining the reads. The PathoDB is an optional module that provides additional annotation (organism taxonomic lineage, gene loci, protein products) for all sequences identified in the sample. The PathoQC module can be used to preprocess the reads prior to alignment with PathoMap.

 Please refer to the following papers: 
 1. "Pathoscope: Species identification and strain attribution with unassembled sequencing data" at http://genome.cshlp.org/content/23/10/1721
-
-2. "PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples" at http://www.microbiomejournal.com/content/2/1/33
++ "PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples" at http://www.microbiomejournal.com/content/2/1/33

 1. Installation
 ---------------

Home modified by Solaiappan Manimaran

Solaiappan Manimaran — Thu, 20 Nov 2014 04:51:32 -0000

--- v9
+++ v10
@@ -6,10 +6,10 @@

 Pathoscope 2.0 consists of four core and two optional analysis modules for sequencing-based metagenomic profiling. The PathoLib module extracts genome reference libraries (target or host/filter) from all available sequences in the NCBI Nucleotide database that belong to a user-defined taxonomic clade. The PathoMap module aligns the reads to the target reference library and removes any reads that have sequence similarity with the host or filter genomes. PathoID resolves read ambiguity, identifies which of the target genomes are present in the sample and estimates the proportions of reads originating from each genome. PathoReport provides two report files: 1) a summary report (.tsv) that contains the numbers and proportions of reads aligned to each genome identified in the sample, and 2) detailed report (.xml) including read coverage, read assignments, and contiguous sequences generated by combining the reads. The PathoDB is an optional module that provides additional annotation (organism taxonomic lineage, gene loci, protein products) for all sequences identified in the sample. The PathoQC module can be used to preprocess the reads prior to alignment with PathoMap.

-Please refer to the following papers 
+Please refer to the following papers: 
 1. "Pathoscope: Species identification and strain attribution with unassembled sequencing data" at http://genome.cshlp.org/content/23/10/1721

-+ "PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples" at http://www.microbiomejournal.com/content/2/1/33
+2. "PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples" at http://www.microbiomejournal.com/content/2/1/33

 1. Installation
 ---------------

Home modified by Solaiappan Manimaran

Solaiappan Manimaran — Thu, 20 Nov 2014 04:49:16 -0000

--- v8
+++ v9
@@ -6,7 +6,10 @@

 Pathoscope 2.0 consists of four core and two optional analysis modules for sequencing-based metagenomic profiling. The PathoLib module extracts genome reference libraries (target or host/filter) from all available sequences in the NCBI Nucleotide database that belong to a user-defined taxonomic clade. The PathoMap module aligns the reads to the target reference library and removes any reads that have sequence similarity with the host or filter genomes. PathoID resolves read ambiguity, identifies which of the target genomes are present in the sample and estimates the proportions of reads originating from each genome. PathoReport provides two report files: 1) a summary report (.tsv) that contains the numbers and proportions of reads aligned to each genome identified in the sample, and 2) detailed report (.xml) including read coverage, read assignments, and contiguous sequences generated by combining the reads. The PathoDB is an optional module that provides additional annotation (organism taxonomic lineage, gene loci, protein products) for all sequences identified in the sample. The PathoQC module can be used to preprocess the reads prior to alignment with PathoMap.

-Please refer to the paper titled "Pathoscope: Species identification and strain attribution with unassembled sequencing data" at http://genome.cshlp.org/content/23/10/1721
+Please refer to the following papers 
+1. "Pathoscope: Species identification and strain attribution with unassembled sequencing data" at http://genome.cshlp.org/content/23/10/1721
+
++ "PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples" at http://www.microbiomejournal.com/content/2/1/33

 1. Installation
 ---------------

Home modified by Solaiappan Manimaran

Solaiappan Manimaran — Wed, 23 Apr 2014 15:28:19 -0000

--- v7
+++ v8
@@ -6,7 +6,7 @@

 Pathoscope 2.0 consists of four core and two optional analysis modules for sequencing-based metagenomic profiling. The PathoLib module extracts genome reference libraries (target or host/filter) from all available sequences in the NCBI Nucleotide database that belong to a user-defined taxonomic clade. The PathoMap module aligns the reads to the target reference library and removes any reads that have sequence similarity with the host or filter genomes. PathoID resolves read ambiguity, identifies which of the target genomes are present in the sample and estimates the proportions of reads originating from each genome. PathoReport provides two report files: 1) a summary report (.tsv) that contains the numbers and proportions of reads aligned to each genome identified in the sample, and 2) detailed report (.xml) including read coverage, read assignments, and contiguous sequences generated by combining the reads. The PathoDB is an optional module that provides additional annotation (organism taxonomic lineage, gene loci, protein products) for all sequences identified in the sample. The PathoQC module can be used to preprocess the reads prior to alignment with PathoMap.

-Please refer to the paper titled "Pathoscope: Species identification and strain attribution with unassembled sequencing data" at http://genome.cshlp.org/content/23/10/1721.
+Please refer to the paper titled "Pathoscope: Species identification and strain attribution with unassembled sequencing data" at http://genome.cshlp.org/content/23/10/1721

 1. Installation
 ---------------