enasequence · corneliusroemer · Oct 5, 2023
diff --git a/conf.py b/conf.py
@@ -85,7 +85,7 @@
 # html_theme = 'alabaster'
 # Jasmine addition: please note that the theme is now specified in the requirements file as sphinx_rtd_theme
 # Jasmine addition: please note that any docs breaking could be due to a required package changing
-# Jasmine addition: it is reccommended to pin requirments - see https://docs.readthedocs.io/en/stable/guides/rep>
+# Jasmine addition: it is recommended to pin requirements - see https://docs.readthedocs.io/en/stable/guides/rep>
 html_theme = "sphinx_rtd_theme"
 
 # marc addition: from http://stackoverflow.com/questions/18969093/how-to-include-the-toctree-in-the-sidebar-of-each-page

diff --git a/faq/umbrella.rst b/faq/umbrella.rst
@@ -162,7 +162,7 @@ The file umbrella_modified.xml should look very similar to the umbrella.xml used
 The 'TITLE', DESCRIPTION' and 'alias' should be the same. 
 This time, the 'RELATED PROJECTS' block should be made up of any new projects you would like to add to the umbrella.
 For example, to add a single project to your umbrella, you should include a single <CHILD_PROJECT> block specifying the project to be added. 
-You do not need to include the full list of exisiting child projects when updating your umbrella project, you only need to include new projects to be added.
+You do not need to include the full list of existing child projects when updating your umbrella project, you only need to include new projects to be added.
 
 Please note that projects can not be removed from an umbrella by modifying this XML and if you need to remove any projects from your umbrella, please `contact us <https://www.ebi.ac.uk/ena/browser/support>`_.
 

diff --git a/retrieval/advanced-search.rst b/retrieval/advanced-search.rst
@@ -67,7 +67,7 @@ Locate all read data submitted for Neanderthals
 
 11. You can use the 'Available Fields' box to choose any fields you wish to see
     included in the table of results. Not all of these will always be relevant.
-    For this serach, we have selected the FASTQ Files preset, but if you skip
+    For this search, we have selected the FASTQ Files preset, but if you skip
     this step you will still be shown a list of accessions with descriptions,
     by default
 

diff --git a/retrieval/ena-project.rst b/retrieval/ena-project.rst
@@ -174,7 +174,7 @@ recommended or optional metadata that was required during registration of that s
 metadata of samples to make it easier to interpret and search across them.
 
 These checklists are developed with the help of research communities themselves to encourage submitters to provide at
-least the minimum information for their samples to be findable and re-usable for further research.
+least the minimum information for their samples to be findable and reusable for further research.
 You can see the full list of checklists `here <https://www.ebi.ac.uk/ena/browser/checklists>`_.
 
 If you want to search for a particular type of sample (e.g. a soil sample), you can search across the archive by

diff --git a/retrieval/file-download.rst b/retrieval/file-download.rst
@@ -85,7 +85,7 @@ from `GitHub <https://github.com/enasequence/ena-ftp-downloader/tree/master/comm
 You can submit one or more comma separated accessions, or a file with accessions that you
 want to download data for. This tool allows downloading of read and analysis files,
 using FTP or Aspera. It has an easy to use interactive interface and can also create
-a script which can be run programatically or integrated with pipelines.
+a script which can be run programmatically or integrated with pipelines.
 
 Download the latest version from
 `ENA Tools <http://ftp.ebi.ac.uk/pub/databases/ena/tools/ena-file-downloader.zip>`_.

diff --git a/retrieval/programmatic-access/browser-api.rst b/retrieval/programmatic-access/browser-api.rst
@@ -3,7 +3,7 @@ How to Download Records using the ENA Browser API
 =================================================
 
 The `ENA Browser API <https://www.ebi.ac.uk/ena/browser/api/>`_ can be used to download ENA Records in EMBL flat file,
-fasta or XML format dependant on the record type.
+fasta or XML format dependent on the record type.
 
 +-----------------------+-------------------------------------------------+
 | **File Format**       | **Available Record Types**                      |

diff --git a/submit/analyses/bionano-maps.md b/submit/analyses/bionano-maps.md
@@ -95,7 +95,7 @@ create subdirectories and upload your files there.
 
 You should then describe these data files in your analysis XML with the `<FILE>` element.
 
-To descibe files required for submission, the analysis object has a `<FILES>` block. 
+To describe files required for submission, the analysis object has a `<FILES>` block. 
 This submits the data files into the archive.
 
 For example:

diff --git a/submit/analyses/pacbio-methylation.md b/submit/analyses/pacbio-methylation.md
@@ -100,7 +100,7 @@ create subdirectories and upload your files there.
 
 You should then describe these data files in your analysis XML with the `<FILE>` element.
 
-To descibe files required for submission, the analysis object has a `<FILES>` block. 
+To describe files required for submission, the analysis object has a `<FILES>` block. 
 This submits the data files into the archive.
 
 For example:

diff --git a/submit/analyses/read-alignments.md b/submit/analyses/read-alignments.md
@@ -27,7 +27,7 @@ Here is an example of a  read alignment analysis XML:
     <ANALYSIS alias="AD0370_C_alignment">
         <TITLE>The Anopheles gambiae 1000 Genomes Project - Phase 1 - Alignment - Crosses</TITLE>
         <DESCRIPTION>Sequence alignments from the AR3 data release from the Anopheles 1000 genomes
-            project. Aligments are in bam format and are presented for each of the 80 A. gambiae
+            project. Alignments are in bam format and are presented for each of the 80 A. gambiae
             specimens comprising parents and progeny of four crosses.</DESCRIPTION>
         <STUDY_REF accession="ERP020641"/>
         <SAMPLE_REF accession="ERS150992"/>
@@ -138,7 +138,7 @@ create subdirectories and upload your files there.
 
 You should then describe these data files in your analysis XML with the `<FILE>` element.
 
-To descibe files required for submission, the analysis object has a `<FILES>` block. 
+To describe files required for submission, the analysis object has a `<FILES>` block. 
 This submits the data files into the archive.
 
 For example:

diff --git a/submit/analyses/sequence-annotation.md b/submit/analyses/sequence-annotation.md
@@ -94,7 +94,7 @@ create subdirectories and upload your files there.
 
 You should then describe these data files in your analysis XML with the `<FILE>` element.
 
-To descibe files required for submission, the analysis object has a `<FILES>` block. 
+To describe files required for submission, the analysis object has a `<FILES>` block. 
 This submits the data files into the archive.
 
 For example:

diff --git a/submit/assembly.rst b/submit/assembly.rst
@@ -8,7 +8,7 @@ Introduction
 
 
 To submit genome or transcriptome assemblies to ENA you must also provide some metadata to 
-describe your research project. This helps make your data re-useable and searchable.
+describe your research project. This helps make your data reusable and searchable.
 
 .. image:: images/metadata_model_assembly.png
    :align: center

diff --git a/submit/fileprep/assembly.rst b/submit/fileprep/assembly.rst
@@ -115,7 +115,7 @@ Please read on for information on the content of the chromosome list file column
    - Topology is not a separate column but can be specified as a modifier to the chromosome type
    - Options are 'linear' or 'circular', default is linear
    - Must not conflict with any value specified in flat file
-   - Contigs, scaffolds and transcriptome sequences are always linear: entering 'circular' here will be overriden
+   - Contigs, scaffolds and transcriptome sequences are always linear: entering 'circular' here will be overridden
 
 - **CHROMOSOME_LOCATION** (optional fourth column): By default eukaryotic chromosomes will be assumed to reside in the
   nucleus and prokaryotic chromosomes and plasmids in the cytoplasm. Allowed values:

diff --git a/submit/fileprep/flatfile_user_manual.txt b/submit/fileprep/flatfile_user_manual.txt
@@ -196,8 +196,8 @@ of the entry. Each entry belongs to exactly one data class.
   PAT            Patent
   EST            Expressed Sequence Tag
   GSS            Genome Survey Sequence
-  HTC            High Thoughput CDNA sequencing
-  HTG            High Thoughput Genome sequencing
+  HTC            High Throughput CDNA sequencing
+  HTG            High Throughput Genome sequencing
   WGS            Whole Genome Shotgun
   TSA            Transcriptome Shotgun Assembly
   STS            Sequence Tagged Site

diff --git a/submit/fileprep/reads.md b/submit/fileprep/reads.md
@@ -30,7 +30,7 @@ However, please note that a variety of other data formats are supported as well.
 
 Reads for different samples should be submitted using separate files. The
 only exception is when a `BAM` or `CRAM` file contains reads for a large
-number of samples intented to be always analysed together. In this case
+number of samples intended to be always analysed together. In this case
 the sample associated with the read file should describe the sample
 group while the `BAM` or `CRAM` file should identify the sample
 for each read.

diff --git a/submit/general-guide/programmatic.md b/submit/general-guide/programmatic.md
@@ -26,7 +26,7 @@ When you are using the test service the receipt XML will contain the following m
 ```
 
 It is advisable to first test your submissions using the Webin test service before
-establising an automated submission pipeline.
+establishing an automated submission pipeline.
 
 ## Webin Rest V2 API
 
@@ -301,9 +301,9 @@ Below is an example of a submission XML used to cancel objects:
 ### Submission XML: request a receipt XML
 
 The `RECEIPT` action can be used to request a receipt XML issued as a result of an `ADD` action
-that contains all the issued accession numbers. This is expecially useful in cases where the
+that contains all the issued accession numbers. This is especially useful in cases where the
 submission request times out before it has as completed. The submission process will continue
-neverthless and the issued accession numbers can be later requested using the `RECEIPT` action.
+nevertheless and the issued accession numbers can be later requested using the `RECEIPT` action.
 
 ```
 SUBMISSION_SET>

diff --git a/submit/general-guide/webin-cli.md b/submit/general-guide/webin-cli.md
@@ -260,7 +260,7 @@ The following formats are supported for [read submissions](../reads/webin-cli):
 - FASTQ: fastq file
 
 
-##### Info File (for backward compability only)
+##### Info File (for backward compatibility only)
 
 You can also provide the metadata fields in a separate info file. The info file has the same format as the manifest file.
 

diff --git a/submit/reads.rst b/submit/reads.rst
@@ -6,7 +6,7 @@ Introduction
 ============
 
 To submit raw read sequencing data to ENA you must also provide some metadata to describe your sequencing project.
-This helps make your data re-useable and searchable.
+This helps make your data reusable and searchable.
 
 .. image:: images/metadata_model_reads.png
    :align: center

diff --git a/submit/reads/programmatic.rst b/submit/reads/programmatic.rst
@@ -24,7 +24,7 @@ Both run and experiment are associated with other objects.
 An experiment is part of a study. Studies are used to group together experiments to
 allow them to be cited together in a publication.
 
-An experiment is assocated with a sample. It is common to have multiple libraries
+An experiment is associated with a sample. It is common to have multiple libraries
 and sequencing experiments for a single sample. Experiments point to samples to
 allow sharing of sample information between multiple experiments.
 

diff --git a/submit/sequence/annotation-checklists.rst b/submit/sequence/annotation-checklists.rst
@@ -186,7 +186,7 @@ Large-Scale Data Checklists
 |                        |              | | location in the genome is mapped.                                          |
 +------------------------+--------------+------------------------------------------------------------------------------+
 | | Genome Survey        | ERT000024    | | For submission of Genome Survey Sequences (GSS). These                     |
-| | Sequence (GSS)       |              | | are short DNA sequences which inlude: random single                        |
+| | Sequence (GSS)       |              | | are short DNA sequences which include: random single                        |
 |                        |              | | pass genome survey sequences, single pass reads from                       |
 |                        |              | | cosmid/BAC/YAC ends (may be chromosome specific), exon                     |
 |                        |              | | trapped genomic sequences, Alu PCR sequences and                           |