fixed english

viramp-docs/ec2_import.rst

@@ -1,27 +1,27 @@
 Custom installation of the VirAmp AMI
 ====================================
 
-Go to http://aws.amazon.com/, in a Web browser.
+Access  http://aws.amazon.com/, in a Web browser.
 
 Select 'My Account/Console' on the top right if you already have an account; otherwise sign up with a new account.
 
 Go to the 'AWS Management Console' option, click the 'EC2' at upper left.
 
-Before importing the AMI, make sure you are in the right Availability zone. Amazon EC2 is hosted in multiple locations world-wide with multiple Availability zones, and resources cannot replicated across regions until specified.  Our AMI is stored at region "US East(N. Virginia)". Check the upper right corner next to your account name, and make sure it's set at the right region. If not, just click and select the right one on from the dropdown menu.
+Before importing the AMI, make sure you are in the right Availability zone. Amazon EC2 is hosted in multiple locations world-wide with multiple Availability zones, and resources cannot be replicated across regions until specified.  Our AMI is stored in region "US East(N. Virginia)". Check the upper right corner next to your account name, and make sure it's set at the correct region. If not, just click and select the correct one on from the dropdown menu.
 
-Next, click the blue button 'Launch Instance'.
+Next, click the blue 'Launch Instance' button.
 
 Step-1: Choosing the instance
 -----------------------------
 
-Click the Community AMIs tab at mid-left and simply search "viramp"
+Click the Community AMIs tab at mid-left and simply search "Szpara_Viramp"
 
 .. image:: viramp-doc/search-ami.png
 
 Step-2: Review Instance type
 -----------------------------
 
-Due to storage and computational requirements, free tier instances are not usable with our AMI. For trial runs it is possible to choose smaller instance types, but for serious usage, it is advised to select at least the m3.large (third option)
+Due to storage and computational requirements, free tier instances are not usable with our AMI. For trial runs it is possible to choose smaller instance types, but for serious usage it is advised to select at least the m3.large (third option)
 
 .. image:: viramp-doc/review-instance-type.png
 
@@ -33,16 +33,10 @@ Step-4: Create Key-pairs
 -----------------------------
 .. image:: viramp-doc/key-pair.png
 
-Congratulations you have successfully launched your own version of the instance.  For information on logging in and starting your instance, please go to :ref:`VirAmp instance login <viramp_login_ref>`
+You have nowsuccessfully launched your own version of the instance.  For information on logging in and starting your instance, please go to :ref:`VirAmp instance login <viramp_login_ref>`
 
 Login to your VirAmp instance and start the server
-------------------------------------------------
-
-At this point you have successfully launched your own version of the VirAmp ins\
-tance, so what's next?
-
-Start exploring the VirAmp platform
-------------------------------------
+----------------------------
 
 Open viramp from a browser, typing in public_IP:8080 (for example, the demo is \
 viramp.com:8080). The public_IP is the IP assigned to your instance, and by def\
@@ -60,7 +54,7 @@ n to the instance are provided at the console.
 
 .. image:: viramp-doc/connect-info.png
 
-Hit the "Connect" buttom to view information you need to login to the backend o\
+Hit the "Connect" button to view information you need to login to the backend o\
 f the system.
 
 .. image:: viramp-doc/connect.png
@@ -81,10 +75,8 @@ Change viramp settings:
 
         ``vi universe_wsgi.ini``
 
-        Line 596: admin_users = dwr19@psu.edu should be changed to reflect the \
-current administrators email address
-        Line 662: ftp_upload_site = viramp.com should be changed from viramp.co\
-m to your public ip address
+        Line 596: admin_users = dwr19@psu.edu should be changed to reflect the current administrators email address
+        Line 662: ftp_upload_site = viramp.com should be changed from viramp.com to your public ip address
 
 Start the viramp server:
 

viramp-docs/variation_assess.rst

@@ -1,11 +1,11 @@
 Post-Assembly Analysis
 =====================
 
-VirAmp not only provides all the processes related with assembly, but also integrates multiple tools for post-assembly processing including quality assessment and variation analysis.
+VirAmp not only provides all the processes related to assembly, but also integrates multiple tools for post-assembly processing including quality assessment and variation analysis.
 
 QUAST REPORT
 ------------
-It is important to evaluate how robust the new assembly is before feeded it into the downstream functional analysis.  VirAmp first provides a report of common assembly evaluation metrics based on comparisons with the reference. A detailed `QUAST report <http://bioinf.spbau.ru/quast>`_ can be downloaded.
+It is important to evaluate how robust the new assembly is before it is feed into the downstream functional analysis.  VirAmp provides a report of common assembly evaluation metrics based on comparisons with the reference. A detailed `QUAST report <http://bioinf.spbau.ru/quast>`_ can be downloaded for further evaluation.
 
 The inputs required are the reference genome and newly created assembly.
 
@@ -37,25 +37,20 @@ VirAmp provides information about the difference between the reference and new a
 Circos graph visualization
 --------------------------
 
-Circos graphs are created as a way to help the user visualize the above alignment. Circos projects the assembled draft genome to the aligned part of reference, creating a straightforward visualization for large structural variation.
+Circos projects the assembled draft genome to the aligned part of the reference genome, creating a straightforward visualization for the above alignment and providing insight into large structural variations.
 
 .. image:: assess-pic/comparison_circos.png
 
 SNP analysis
 -------------
 
-With the alignment between assembly and reference, SNP information is also provided in VCF format.
+Using the alignment between the assembly and the reference, SNP information is  displayed in VCF format.
 
 .. image:: assess-pic/snp.png
 
 Repeat and Tandem repeat analysis
 ---------------------------------
 
-By aligning the assembly against itself, VirAmp also provides repeat and tandem repeat information. The starting coordinates and length are dervied from this alignment.
+By aligning the assembly against itself, VirAmp additionally provides repeat and tandem repeat information. The starting coordinates and lengths of the repeats are dervied from this alignment.
 
 .. image:: assess-pic/tandem-repeat.png
-
-BWA aligner
------------
-
-Besides all the specific tools listed above, general tools like `bwa <http://bio-bwa.sourceforge.net/>`_ are also provided for use.

viramp-docs/viramp_intro.rst

@@ -17,7 +17,7 @@ Next we provide a chronological introduction of each step in the pipeline.
 
 Quality Control
 ---------------
-First, trim out the low quality bases of the input fastq files. This can be achieved either by removing low quality bases or mandatorily trimming a certain length from each end.
+First, trim out the low quality bases of the input fastq files. This can be achieved either by removing low quality bases or trimming a certain length from each end.
 
 .. image:: manual-pic/trim_qual.png
 
@@ -29,7 +29,7 @@ Next, reduce coverage and bias using `Digital normalization <http://ged.msu.edu/
 
 `de novo` Contig assembly
 ------------------------
-Next, the pipeline assembles the short reads into longer contigs, by default the **One-click pipeline** uses `velvet <https://www.ebi.ac.uk/~zerbino/velvet/>`_. Two alternatives, `SPAdes <http://bioinf.spbau.ru/spades>`_ and `VICUNA <http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna>`_ , are provided and can be selected either as individual tools or through the advanced options in the one-click pipeline.
+Next, the pipeline assembles the short reads into longer contigs. By default the **One-click pipeline** uses `velvet <https://www.ebi.ac.uk/~zerbino/velvet/>`_. Two alternatives, `SPAdes <http://bioinf.spbau.ru/spades>`_ and `VICUNA <http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna>`_ , are provided and can be selected as either individual tools or through the advanced options in the one-click pipeline.
 
 .. image:: manual-pic/de-novo.png
 
@@ -41,13 +41,13 @@ Next, the contigs are assembled into even longer `super-contigs`. This step is a
 
 Reference-independent scaffolding
 ---------------------------------
-This step extends the super-contigs and connects them using `SSPACE <http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/>`_.  At the end of this step, the pipeline will produce a draft genome, which is a multi-fasta usually contains 5~15 contigs, listed in the same order as the reference.
+This step extends the super-contigs and connects them using `SSPACE <http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/>`_.  At the end of this step, the pipeline will produce a draft genome. This draft genome is a multi-fasta file usually containing 5~15 contigs which are listed in the same order as the reference.
 
 .. image:: manual-pic/sspace.png
 
 Gap closing
 -----------
-This step connects all the contigs in the multi-fasta from the previous step into one linear genome. This is for the convenience of downstream functional analysis.  However, this is **optional** and highly recommended to be done only after assessing the draft genome, as the gaps between the contigs could from misassembly, sequencing, genome feature, etc. 
+This step connects all the contigs in the multi-fasta from the previous step into one linear genome for the convenience of downstream functional analysis.  However, this is **optional** and highly recommended to be done only after assessing the draft genome, as the gaps between the contigs could be from misassembly, sequencing, genome feature, etc. 
 
 .. image:: manual-pic/linear.png