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Home modified by Renato Oliveira

Renato Oliveira — Mon, 13 Aug 2018 14:24:09 -0000

--- v13
+++ v14
@@ -7,6 +7,10 @@
 * Use nano/vi to change FORWARD & REVERSE folders into the pipebar shell script. 
 * FORWARD & REVERSE folders must contain its corresponding AB1 files.
 * Version 3.0.
+
+### How to Cite###
+If you use Pipebar or OverlapPER, please, cite:
+Oliveira, R. R. M., Nunes, G. L., de Lima, T. G. L., Oliveira, G., & Alves, R. (2018). PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly. BMC Bioinformatics, 19(1). doi:10.1186/s12859-018-2307-y

 ### How do I get set up? ###
 To facilitate the use of PIPEBAR by the users, we created a docker image which will enable the user to

Home modified by Renato Oliveira

Renato Oliveira — Wed, 13 Jun 2018 16:35:20 -0000

--- v12
+++ v13
@@ -1,12 +1,12 @@
 # Pipebar: a fast and accurate pipeline for DNA barcoding analysis #

-It runs a barcode pipeline to assemble Sanger files (.AB1).
+It runs a barcode pipeline to assemble Sanger (.AB1), FASTQ or FASTA files.

 ### How does it work? ###

 * Use nano/vi to change FORWARD & REVERSE folders into the pipebar shell script. 
 * FORWARD & REVERSE folders must contain its corresponding AB1 files.
-* Version 1.0.
+* Version 3.0.

 ### How do I get set up? ###
 To facilitate the use of PIPEBAR by the users, we created a docker image which will enable the user to
@@ -43,19 +43,48 @@
 At this point you will be enabled to run the pipeline, as it follows.

 ~~~
-./pipebar <separator_of_forward reverse_reads=""> <min_overlap> <min_similarity>
-<phred_offset> <phred_threshold> <"coding" or "non-coding" sequence> <"full" or "fast" report>
+./pipebar --format <"ab1", "fastq" or "fastaqual"> --sep <separator_of_forward reverse_reads=""> --mo <min_overlap> --ms <min_similarity> --phred <phred_offset> -q <phred_threshold> --coding <"1" for coding sequences or "0" for non-coding" sequence> --gcode <"1" for Standard code, "2" to Vertebrate Mitochondrial Code, "5" to Invertebrate Mitochondrial Code or "11" to Bacterial, Archaeal and Plant plastid code> --rep <"full" or "fast" report>
 ~~~

-ex.: ./pipebar _ 25 0.9 33 20 coding fast
+ex.: ./pipebar --format ab1 --sep _ --mo 25 --ms 0.9 --phred 33 -q 20 --coding 1 --gcode 1 --rep fast

-* <separator_of_forward reverse_reads="">: The IDs from both forward and reverse reads must have a separator. ex: 001read_forward and 001read_reverse have "_" as separator;
-* <min_overlap>: length of the minimum overlap between the paired reads (Default 25);
-* <min_similarity>: percentage of the accepted minimum similarity between an overlap region of two paired reads;
-* <phred_offset>: The offset of the PHRED qualities codes used (33 or 64);
-* <phred_threshold>: The minimum quality value for trimming and filtering steps;
-* <"coding" or "non-coding" sequence>: Inform if the barcode sequences to be analyzed are from coding (e.g. rbcL, matK) or non-coding (e.g. ITS, atpF-trnH) regions;
-* <"full" or "fast" report>: A full report will generate a quality graphical report for each barcode sequence analyzed, while a fast report will generate an overview of the analyzed barcodes in one single report.
+Options:
+
+    -h|--help  
+        Show this output.
+    -V|--version
+        Show version information.
+    --format <string>
+        Input format. Can be "ab1", "fastq" or "fastaqual".
+    --sep <string>
+        The IDs from both forward and reverse reads must have a separator.
+        Ex: 001read_forward and 001read_reverse have "_" (default) as 
+        separator
+    --mo <integer>
+        Length of the minimum overlap between the paired reads (default is 25).
+    --ms <float>
+        Percentage of the accepted minimum similarity in an overlap region of
+        two paired reads (default is 0.9).
+    --phred <integer>
+        The offset of the PHRED qualities codes used. 
+        Can be 33 or 64 (default is 33).
+    -q <integer>
+        The minimum quality value for trimming and 
+        filtering steps (default is 20).
+    --coding <integer>
+        Inform if the barcode sequences to be analyzed are from 
+        coding (e.g. rbcL, matK) or non-coding (e.g. ITS, atpF-trnH) regions.
+        Inform "1" for coding or "0" for non-coding sequences (default is 1)
+    --gcode <integer>
+        The genetic code to be used when translating the nucleotide
+        sequences into protein, when it comes to a coding region. It can be
+        "1" to Standard Code, "2" to Vertebrate Mitochondrial Code,
+        "5" to Invertebrate Mitochondrial Code or "11" to Bacterial, Archaeal
+        and Plant plastid code.
+    --rep <string>
+        A full report will generate a quality graphical report for each 
+        barcode sequence analyzed, while a fast report will generate an overview 
+        of the analyzed barcodes in one single report (default is "fast")

 When the pipeline finishes its execution, you need to exit the pipebar environment, just enter:
 `exit`
@@ -84,32 +113,54 @@
 - **fastx_toolkit**: http://hannonlab.cshl.edu/fastx_toolkit/
 - **BBmap**: https://sourceforge.net/projects/bbmap/?source=typ_redirect
 - **FastQC**: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-- **OverlapPER**: https://sourceforge.net/projects/pipebar/files/overlapper.py/download
+- **OverlapPER**: https://sourceforge.net/projects/overlapper-reads/files/OverlapPER-1.5.tar.gz/download

 #####Step 1 - Running Pipebar
 At this point you will be enabled to run the pipeline, as it follows.

 ~~~
-./pipebar <separator_of_forward reverse_reads=""> <min_overlap> <min_similarity>
-<phred_offset> <phred_threshold> <"coding" or "non-coding" sequence> <"full" or "fast"
-report>
+./pipebar --format <"ab1", "fastq" or "fastaqual"> --sep <separator_of_forward reverse_reads=""> --mo <min_overlap> --ms <min_similarity> --phred <phred_offset> -q <phred_threshold> --coding <"1" for coding sequences or "0" for non-coding" sequence> --gcode <"1" for Standard code, "2" to Vertebrate Mitochondrial Code, "5" to Invertebrate Mitochondrial Code or "11" to Bacterial, Archaeal and Plant plastid code> --rep <"full" or "fast" report>
 ~~~
-ex.: ./pipebar _ 25 0.9 33 20 coding fast
+ex.: ./pipebar --format ab1 --sep _ --mo 25 --ms 0.9 --phred 33 -q 20 --coding 1 --gcode 1 --rep fast

-* <separator_of_forward reverse_reads="">: The IDs from both forward and reverse
-* reads must have a separator. ex: 001read_forward and 001read_reverse have "_" as
-* separator;
-* <min_overlap>: length of the minimum overlap between the paired reads (Default 25);
-* <min_similarity>: percentage of the accepted minimum similarity between an overlap
-* region of two paired reads;
-* <phred_offset>: The offset of the PHRED qualities codes used (33 or 64);
-* <phred_threshold>: The minimum quality value for trimming and filtering steps;
-* <"coding" or "non-coding" sequence>: Inform if the barcode sequences to be analyzed
-* are from coding (e.g. rbcL, matK) or non-coding (e.g. ITS, atpF-trnH) regions;
-* <"full" or "fast" report>: A full report will generate a quality graphical report for each
-* barcode sequence analyzed, while a fast report will generate an overview of the
-* analyzed barcodes in one single report.
+ Options:
+
+    -h|--help  
+        Show this output.
+    -V|--version
+        Show version information.
+    --format <string>
+        Input format. Can be "ab1", "fastq" or "fastaqual".
+    --sep <string>
+        The IDs from both forward and reverse reads must have a separator.
+        Ex: 001read_forward and 001read_reverse have "_" (default) as 
+        separator
+    --mo <integer>
+        Length of the minimum overlap between the paired reads (default is 25).
+    --ms <float>
+        Percentage of the accepted minimum similarity in an overlap region of
+        two paired reads (default is 0.9).
+    --phred <integer>
+        The offset of the PHRED qualities codes used. 
+        Can be 33 or 64 (default is 33).
+    -q <integer>
+        The minimum quality value for trimming and 
+        filtering steps (default is 20).
+    --coding <integer>
+        Inform if the barcode sequences to be analyzed are from 
+        coding (e.g. rbcL, matK) or non-coding (e.g. ITS, atpF-trnH) regions.
+        Inform "1" for coding or "0" for non-coding sequences (default is 1)
+    --gcode <integer>
+        The genetic code to be used when translating the nucleotide
+        sequences into protein, when it comes to a coding region. It can be
+        "1" to Standard Code, "2" to Vertebrate Mitochondrial Code,
+        "5" to Invertebrate Mitochondrial Code or "11" to Bacterial, Archaeal
+        and Plant plastid code.
+    --rep <string>
+        A full report will generate a quality graphical report for each 
+        barcode sequence analyzed, while a fast report will generate an overview 
+        of the analyzed barcodes in one single report (default is "fast")

 #####Step 2 - Getting the Results
 The resulting files are:

Home modified by Renato Oliveira

Renato Oliveira — Mon, 13 Nov 2017 19:03:22 -0000

--- v11
+++ v12
@@ -72,8 +72,8 @@
 * TrimmedStop_DNA.fasta;
 * TrimmedStop_Prot.fasta;
 * fastqc_report;
-* *overlapped_fastqc.html;
-* *overlapped_fastqc.zip;
+* * overlapped_fastqc.html;
+* * overlapped_fastqc.zip;

@@ -122,8 +122,8 @@
 * TrimmedStop_DNA.fasta
 * TrimmedStop_Prot.fasta
 * fastqc_report
-* *overlapped_fastqc.html;
-* *overlapped_fastqc.zip;
+* * overlapped_fastqc.html;
+* * overlapped_fastqc.zip;

 [[members limit=20]]

Home modified by Renato Oliveira

Renato Oliveira — Mon, 13 Nov 2017 19:02:56 -0000

--- v10
+++ v11
@@ -72,8 +72,8 @@
 * TrimmedStop_DNA.fasta;
 * TrimmedStop_Prot.fasta;
 * fastqc_report;
-* * overlapped_fastqc.html;
-* * overlapped_fastqc.zip;
+* *overlapped_fastqc.html;
+* *overlapped_fastqc.zip;

@@ -122,8 +122,9 @@
 * TrimmedStop_DNA.fasta
 * TrimmedStop_Prot.fasta
 * fastqc_report
-* * overlapped_fastqc.html
-* * overlapped_fastqc.zip
+* *overlapped_fastqc.html;
+* *overlapped_fastqc.zip;
+

 [[members limit=20]]
 [[download_button]]

Home modified by Renato Oliveira

Renato Oliveira — Mon, 13 Nov 2017 19:02:12 -0000

--- v9
+++ v10
@@ -63,6 +63,7 @@
 #####Step 6 - Getting the Results
 The pipebar script saves the results in the ResultPipebar folder that is in the same directory
 from where it was called. The resulting files are:
+
 * notAssembled-1.fastq;
 * notAssembled-2.fastq;
 * overlaped.fasta;

Home modified by Renato Oliveira

Renato Oliveira — Mon, 13 Nov 2017 19:01:31 -0000

--- v8
+++ v9
@@ -49,19 +49,13 @@

 ex.: ./pipebar _ 25 0.9 33 20 coding fast

-* <separator_of_forward reverse_reads="">: The IDs from both forward and reverse
-* reads must have a separator. ex: 001read_forward and 001read_reverse have "_" as
-* separator;
+* <separator_of_forward reverse_reads="">: The IDs from both forward and reverse reads must have a separator. ex: 001read_forward and 001read_reverse have "_" as separator;
 * <min_overlap>: length of the minimum overlap between the paired reads (Default 25);
-* <min_similarity>: percentage of the accepted minimum similarity between an overlap
-* region of two paired reads;
+* <min_similarity>: percentage of the accepted minimum similarity between an overlap region of two paired reads;
 * <phred_offset>: The offset of the PHRED qualities codes used (33 or 64);
 * <phred_threshold>: The minimum quality value for trimming and filtering steps;
-* <"coding" or "non-coding" sequence>: Inform if the barcode sequences to be analyzed
-* are from coding (e.g. rbcL, matK) or non-coding (e.g. ITS, atpF-trnH) regions;
-* <"full" or "fast" report>: A full report will generate a quality graphical report for each
-* barcode sequence analyzed, while a fast report will generate an overview of the
-* analyzed barcodes in one single report.
+* <"coding" or "non-coding" sequence>: Inform if the barcode sequences to be analyzed are from coding (e.g. rbcL, matK) or non-coding (e.g. ITS, atpF-trnH) regions;
+* <"full" or "fast" report>: A full report will generate a quality graphical report for each barcode sequence analyzed, while a fast report will generate an overview of the analyzed barcodes in one single report.

 When the pipeline finishes its execution, you need to exit the pipebar environment, just enter:
 `exit`
@@ -69,16 +63,16 @@
 #####Step 6 - Getting the Results
 The pipebar script saves the results in the ResultPipebar folder that is in the same directory
 from where it was called. The resulting files are:
-* notAssembled-1.fastq
-* notAssembled-2.fastq
-* overlaped.fasta
-* overlapped.fastq
-* report.pdf
-* TrimmedStop_DNA.fasta
-* TrimmedStop_Prot.fasta
-* fastqc_report
-* * overlapped_fastqc.html
-* * overlapped_fastqc.zip
+* notAssembled-1.fastq;
+* notAssembled-2.fastq;
+* overlaped.fasta;
+* overlapped.fastq;
+* report.pdf;
+* TrimmedStop_DNA.fasta;
+* TrimmedStop_Prot.fasta;
+* fastqc_report;
+* * overlapped_fastqc.html;
+* * overlapped_fastqc.zip;

Home modified by Renato Oliveira

Renato Oliveira — Mon, 13 Nov 2017 18:59:02 -0000

--- v7
+++ v8
@@ -24,27 +24,29 @@

 #####Step 2 – Checking Docker installation
->> sudo docker --version
+`sudo docker --version`

 #####Step 3 – Downloading the Pipebar Script
 In this step, you will download the script, available on SourceForge, that automatize the
 Pipebar pipeline. To download the script, enter:
->>wget https://sourceforge.net/projects/pipebar/files/pipebarScript.sh
+`wget https://sourceforge.net/projects/pipebar/files/pipebarScript.sh`

 #####Step 4 - Initiating Pipebar
 After downloading the script, you will be able to run the pipeline. With superuser permission
 you will type:

->>sudo sh pipebarScript.sh path/to/forward/reads path/to/reverse/reads
+`sudo sh pipebarScript.sh path/to/forward/reads path/to/reverse/reads`
 You need to pass two parameters, the path to forward and reverse reads. Once you entered the
 above command you will get a similar output, regarding the creation of the Pipebar container.

 #####Step 5 - Running Pipebar
 At this point you will be enabled to run the pipeline, as it follows.

->> ./pipebar <separator_of_forward reverse_reads=""> <min_overlap> <min_similarity>
-<phred_offset> <phred_threshold> <"coding" or "non-coding" sequence> <"full" or "fast"
-* report>
+~~~
+./pipebar <separator_of_forward reverse_reads=""> <min_overlap> <min_similarity>
+<phred_offset> <phred_threshold> <"coding" or "non-coding" sequence> <"full" or "fast" report>
+~~~
+
 ex.: ./pipebar _ 25 0.9 33 20 coding fast

 * <separator_of_forward reverse_reads="">: The IDs from both forward and reverse
@@ -62,7 +64,7 @@
 * analyzed barcodes in one single report.

 When the pipeline finishes its execution, you need to exit the pipebar environment, just enter:
->>exit
+`exit`

 #####Step 6 - Getting the Results
 The pipebar script saves the results in the ResultPipebar folder that is in the same directory
@@ -93,9 +95,11 @@
 #####Step 1 - Running Pipebar
 At this point you will be enabled to run the pipeline, as it follows.

->> ./pipebar <separator_of_forward reverse_reads=""> <min_overlap> <min_similarity>
+~~~
+./pipebar <separator_of_forward reverse_reads=""> <min_overlap> <min_similarity>
 <phred_offset> <phred_threshold> <"coding" or "non-coding" sequence> <"full" or "fast"
 report>
+~~~
 ex.: ./pipebar _ 25 0.9 33 20 coding fast

 * <separator_of_forward reverse_reads="">: The IDs from both forward and reverse

Home modified by Renato Oliveira

Renato Oliveira — Mon, 13 Nov 2017 18:57:37 -0000

--- v6
+++ v7
@@ -17,8 +17,11 @@
 usage along PIPEBAR.

 #####Step 1 – Installing Docker and wget (prerequisites)
->> sudo apt-get install docker.io
->> sudo apt-get install wget
+~~~
+sudo apt-get install docker.io
+sudo apt-get install wget
+~~~
+

 #####Step 2 – Checking Docker installation
 >> sudo docker --version

Home modified by Renato Oliveira

Renato Oliveira — Mon, 13 Nov 2017 18:56:04 -0000

--- v5
+++ v6
@@ -9,19 +9,73 @@
 * Version 1.0.

 ### How do I get set up? ###
+To facilitate the use of PIPEBAR by the users, we created a docker image which will enable the user to
+run PIPEBAR without installing its dependencies.

-#### Installation using Docker:
-To facilitate the installation of pipebar for interested users, we created an image on docker that discards the installation of all the tools used in Pipebar.
+####Installation using docker (see https://docs.docker.com):
+A docker image is available so the installation of all required tools are already wraped up for
+usage along PIPEBAR.

-You will need to:
-* Install Docker: 
-    * Linux and MacOS: 
-        1. open the terminal and type "sudo apt-get install docker.io"
-        2. "sudo docker pull itvds-bioinfo/pipebar"
-        3. "sudo docker run -t -i itvds-bioinfo/pipebar /bin/bash"
-        4. "cd /home/pipebar"
-        5. To copy your AB1 files to the forward and reverse files, first you will have to run the docker as demostrated in previous steps. This will generate a container number in the format root@<container>. Use this number as destination to your files: "sudo docker cp your_forward_ab1files/ <container>:/home/pipebar"
-        6. Run "**./pipebar** <separator_of_forward reverse_reads=""> <min_overlap> <min_similarity> <phred_offset>"
+#####Step 1 – Installing Docker and wget (prerequisites)
+>> sudo apt-get install docker.io
+>> sudo apt-get install wget
+
+#####Step 2 – Checking Docker installation
+>> sudo docker --version
+
+#####Step 3 – Downloading the Pipebar Script
+In this step, you will download the script, available on SourceForge, that automatize the
+Pipebar pipeline. To download the script, enter:
+>>wget https://sourceforge.net/projects/pipebar/files/pipebarScript.sh
+
+#####Step 4 - Initiating Pipebar
+After downloading the script, you will be able to run the pipeline. With superuser permission
+you will type:
+
+>>sudo sh pipebarScript.sh path/to/forward/reads path/to/reverse/reads
+You need to pass two parameters, the path to forward and reverse reads. Once you entered the
+above command you will get a similar output, regarding the creation of the Pipebar container.
+
+#####Step 5 - Running Pipebar
+At this point you will be enabled to run the pipeline, as it follows.
+
+>> ./pipebar <separator_of_forward reverse_reads=""> <min_overlap> <min_similarity>
+<phred_offset> <phred_threshold> <"coding" or "non-coding" sequence> <"full" or "fast"
+* report>
+ex.: ./pipebar _ 25 0.9 33 20 coding fast
+
+* <separator_of_forward reverse_reads="">: The IDs from both forward and reverse
+* reads must have a separator. ex: 001read_forward and 001read_reverse have "_" as
+* separator;
+* <min_overlap>: length of the minimum overlap between the paired reads (Default 25);
+* <min_similarity>: percentage of the accepted minimum similarity between an overlap
+* region of two paired reads;
+* <phred_offset>: The offset of the PHRED qualities codes used (33 or 64);
+* <phred_threshold>: The minimum quality value for trimming and filtering steps;
+* <"coding" or "non-coding" sequence>: Inform if the barcode sequences to be analyzed
+* are from coding (e.g. rbcL, matK) or non-coding (e.g. ITS, atpF-trnH) regions;
+* <"full" or "fast" report>: A full report will generate a quality graphical report for each
+* barcode sequence analyzed, while a fast report will generate an overview of the
+* analyzed barcodes in one single report.
+
+When the pipeline finishes its execution, you need to exit the pipebar environment, just enter:
+>>exit
+
+#####Step 6 - Getting the Results
+The pipebar script saves the results in the ResultPipebar folder that is in the same directory
+from where it was called. The resulting files are:
+* notAssembled-1.fastq
+* notAssembled-2.fastq
+* overlaped.fasta
+* overlapped.fastq
+* report.pdf
+* TrimmedStop_DNA.fasta
+* TrimmedStop_Prot.fasta
+* fastqc_report
+* * overlapped_fastqc.html
+* * overlapped_fastqc.zip
+
+

 ####Installing dependencies manually. 
 You will need to download the following packages and install them:
@@ -33,20 +87,41 @@
 - **OverlapPER**: https://sourceforge.net/projects/pipebar/files/overlapper.py/download

-### How to run? ###
+#####Step 1 - Running Pipebar
+At this point you will be enabled to run the pipeline, as it follows.

-* Put your AB1 and PHD.1 files in the respective Forward and Reverse folders.
-* Usage: **./pipebar** <separator_of_forward reverse_reads=""> <min_overlap> <min_similarity> <phred_offset>
-- <separator_of_forward reverse_reads="">: The IDs from both forward and reverse reads must have a separator
-ex: 001read_forward and 001read_reverse have "_" as separator;
-- <min_overlap>: length of the minimum overlap between the paired reads;
-- <min_similarity>: percentage of the accepted minimum similarity between an overlap region of two paired reads;
-- <phred_offset>: The offset of the PHRED qualities codes used (33 or 64);
+>> ./pipebar <separator_of_forward reverse_reads=""> <min_overlap> <min_similarity>
+<phred_offset> <phred_threshold> <"coding" or "non-coding" sequence> <"full" or "fast"
+report>
+ex.: ./pipebar _ 25 0.9 33 20 coding fast

-### Output ###
+* <separator_of_forward reverse_reads="">: The IDs from both forward and reverse
+* reads must have a separator. ex: 001read_forward and 001read_reverse have "_" as
+* separator;
+* <min_overlap>: length of the minimum overlap between the paired reads (Default 25);
+* <min_similarity>: percentage of the accepted minimum similarity between an overlap
+* region of two paired reads;
+* <phred_offset>: The offset of the PHRED qualities codes used (33 or 64);
+* <phred_threshold>: The minimum quality value for trimming and filtering steps;
+* <"coding" or "non-coding" sequence>: Inform if the barcode sequences to be analyzed
+* are from coding (e.g. rbcL, matK) or non-coding (e.g. ITS, atpF-trnH) regions;
+* <"full" or "fast" report>: A full report will generate a quality graphical report for each
+* barcode sequence analyzed, while a fast report will generate an overview of the
+* analyzed barcodes in one single report.

-* The pipeline provides the resulting files overlapped.fastq & overlapped.fasta.
-* The pipeline also provides a full fastqc report.
+#####Step 2 - Getting the Results
+The resulting files are:
+
+* notAssembled-1.fastq
+* notAssembled-2.fastq
+* overlaped.fasta
+* overlapped.fastq
+* report.pdf
+* TrimmedStop_DNA.fasta
+* TrimmedStop_Prot.fasta
+* fastqc_report
+* * overlapped_fastqc.html
+* * overlapped_fastqc.zip

 [[members limit=20]]
 [[download_button]]

Home modified by Renato Oliveira

Renato Oliveira — Mon, 23 Jan 2017 14:23:49 -0000

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