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Nextomics · Oct 9, 2020 · 61f4e05 · 61f4e05
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
-[![Downloads](https://img.shields.io/github/downloads/Nextomics/NextDenovo/total?logo=github)](https://github.com/Nextomics/NextDenovo/releases/download/v2.3.1/NextDenovo.tgz)
+[![Downloads](https://img.shields.io/github/downloads/Nextomics/NextDenovo/total?logo=github)](https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz)
 [![Release](https://img.shields.io/github/release/Nextomics/NextDenovo.svg)](https://github.com/Nextomics/NextDenovo/releases)
-[![Issues](https://img.shields.io/github/issues/Nextomics/NextDenovo.svg)](https://github.com/Nextomics/NextDenovo/issues)
+[![Documentation Status](https://readthedocs.org/projects/nextdenovo/badge/?version=latest)](https://nextdenovo.readthedocs.io/en/latest/?badge=latest)
 
 # NextDenovo
 NextDenovo is a string graph-based *de novo* assembler for long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base accuracy, please use [NextPolish](https://github.com/Nextomics/NextPolish).
@@ -11,7 +11,7 @@ We benchmarked NextDenovo against other assemblers using Oxford Nanopore long re
 
 * **DOWNLOAD**   
 click [here](https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz) or use the following command:   
-`wget https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz`   
+`wget https://github.com/Nextomics/NextDenovo/releases/download/v2.3.1/NextDenovo.tgz`   
 
 	***Note:*** If you get an error like `version 'GLIBC_2.14' not found` or `liblzma.so.0: cannot open shared object file`, Please download [this version](https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo-CentOS6.9.tgz).
 
@@ -30,10 +30,14 @@ click [here](https://github.com/Nextomics/NextDenovo/releases/latest/download/Ne
 
 * [Quick Start](https://nextdenovo.readthedocs.io/en/latest/QSTART.html#quick-start) - no experience required, download and assemble now
 * [Tutorial](https://nextdenovo.readthedocs.io/en/latest/TEST1.html) - step by step introduction to assemble the HG002 genome
-* [FAQ](https://nextdenovo.readthedocs.io/en/latest/FAQ.html) - Frequently asked questions
+* [FAQ](https://nextdenovo.readthedocs.io/en/latest/FAQ.html) - frequently asked questions
 * [Parameter Reference](https://nextdenovo.readthedocs.io/en/latest/OPTION.html) - a detailed introduction about all the parameters
 * [Cite](https://nextdenovo.readthedocs.io/en/latest/QSTART.html#cite) - if you get a good assembly with NextDenovo, please cite it
 
+## Star
+
+You can track updates by tab the `Star` button on the upper-right corner at this page.
+
 ## More
 
-The complete user documentation is available [here](https://nextdenovo.readthedocs.io/en/latest/).
+The complete user documentation is available [here](https://nextdenovo.readthedocs.io/en/latest/).
diff --git a/doc/OPTION.rst b/doc/OPTION.rst
@@ -10,14 +10,14 @@ Input
 
 - ``input_fofn`` (one file one line)
 
-  .. code:: console
+  .. code-block:: shell
 
     ls reads1.fasta reads2.fastq reads3.fasta.gz reads4.fastq.gz ... > input.fofn
 - ``config file``
 
   A config file is a text file that contains a set of parameters (key=value pairs) to set runtime parameters for NextDenovo. The following is a typical config file, which is also located in ``doc/run.cfg``.
 
-  .. code:: console
+  .. code-block:: bash
 
     [General]
     job_type = local
@@ -150,4 +150,4 @@ Assembly options
     minimap2 options, used to map reads back to the assembly.
   .. option::  nextgraph_options = -a 1
 
-    nextgraph options, see :ref:`nextgraph <nextgraph>` for details.  
+    nextgraph options, see :ref:`nextgraph <nextgraph>` for details.  
diff --git a/doc/QSTART.rst b/doc/QSTART.rst
@@ -6,9 +6,12 @@
 .. image:: https://img.shields.io/github/release/Nextomics/NextDenovo.svg
    :target: https://github.com/Nextomics/NextDenovo/releases
    :alt: Version
-.. .. image:: https://img.shields.io/github/issues/Nextomics/NextDenovo.svg
-..    :target: https://github.com/Nextomics/NextDenovo/issues
-..    :alt: Issues
+.. image:: https://img.shields.io/github/issues/Nextomics/NextDenovo.svg
+   :target: https://github.com/Nextomics/NextDenovo/issues
+   :alt: Issues
+.. image:: https://readthedocs.org/projects/nextdenovo/badge/?version=latest
+   :target: https://nextdenovo.readthedocs.io/en/latest/?badge=latest
+   :alt: Documentation Status
 .. .. image:: https://img.shields.io/badge/切换-中文版本-9cf
 ..    :target: https://github.com/Nextomics/NextDenovo/issues
 ..    :alt: 中文版本
@@ -46,7 +49,7 @@ Installation
 
    click `here <https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz>`__ or use the following command:
 
-   .. code:: console
+   .. code-block:: shell
 
       wget https://github.com/Nextomics/NextDenovo/releases/latest/download/NextDenovo.tgz
 
@@ -69,7 +72,7 @@ Installation
 
 -  **TEST**
 
-   .. code:: console
+   .. code-block:: shell
 
       nextDenovo test_data/run.cfg 
 
@@ -79,20 +82,20 @@ Quick Start
 
 #. Prepare input.fofn
 
-   .. code:: console
+   .. code-block:: shell
 
       ls reads1.fasta reads2.fastq reads3.fasta.gz reads4.fastq.gz ... > input.fofn
 #. Create run.cfg
 
-   .. code:: console
+   .. code-block:: shell
 
       cp doc/run.cfg ./
    
    .. note:: Please change the value of seed\_cutoff using :ref:`bin/seq\_stat <seq_stat>` and refer to :ref:`doc/OPTION <options>` to optimize parallel computing parameters.
 
 #. Run
 
-   .. code:: console
+   .. code-block:: shell
 
       nextDenovo run.cfg
 
@@ -132,7 +135,7 @@ Limitations
 Star
 ~~~~
 
-You can track updates by tab the "Star" button on the upper-right corner at the `github page <https://github.com/Nextomics/NextDenovo>`_.
+You can track updates by tab the ``Star`` button on the upper-right corner at the `github page <https://github.com/Nextomics/NextDenovo>`_.
 
 .. |ss| raw:: html
 

diff --git a/doc/TEST1.rst b/doc/TEST1.rst
@@ -5,19 +5,19 @@ Assemble the genome of HG002_NA24385_son using NextDenovo
 
 1. **Download reads**
 
-  .. code:: console
+  .. code-block:: shell
 
     wget https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/Ultralong_OxfordNanopore/final/ultra-long-ont.fastq.gz
 
 2. **Prepare input file (input.fofn)**
 
-   .. code:: console
+   .. code-block:: shell
 
     ls ultra-long-ont.fastq.gz > input.fofn
 
 3. **Calculate the recommended minimum seed length**
 
-  .. code:: console
+  .. code-block:: shell
   
     bin/seq_stat -f 1k -g 3g -d 45 input.fofn > input.fofn.stat
 
@@ -46,7 +46,7 @@ Assemble the genome of HG002_NA24385_son using NextDenovo
 
 4. **Prepare config file (run.cfg)** 
 
-  .. code:: console
+  .. code-block:: shell
 
     [General]
     job_type = sge # here we use SGE to manage jobs
@@ -76,7 +76,7 @@ Assemble the genome of HG002_NA24385_son using NextDenovo
 
 5. **Run**
 
-  .. code:: console
+  .. code-block:: shell
     
     nohup nextDenovo run.cfg &
 

diff --git a/doc/TEST2.rst b/doc/TEST2.rst
@@ -7,19 +7,19 @@ Assessment of the `CHM13 <https://github.com/nanopore-wgs-consortium/CHM13>`__ g
 
 1. **Download reads**
 
-  .. code:: console
+  .. code-block:: shell
 
     wget https://s3.amazonaws.com/nanopore-human-wgs/chm13/nanopore/rel3/rel3.fastq.gz
 
 2. **Prepare input file (input.fofn)**
 
-  .. code:: console
+  .. code-block:: shell
 
     ls rel3.fastq.gz > input.fofn
 
 3. **Calculate the recommended minimum seed length**
 
-  .. code:: console
+  .. code-block:: shell
 
     bin/seq_stat -f 20k -g 3.1g input.fofn > input.fofn.stat
 
@@ -48,7 +48,7 @@ Assessment of the `CHM13 <https://github.com/nanopore-wgs-consortium/CHM13>`__ g
 
 4. **Prepare config file (run.cfg)**
 
-   .. code:: console
+   .. code-block:: shell
 
     [General]
     job_type = sge
@@ -78,7 +78,7 @@ Assessment of the `CHM13 <https://github.com/nanopore-wgs-consortium/CHM13>`__ g
 
 5. **Run**
 
-  .. code:: console
+  .. code-block:: shell
 
     nohup nextDenovo run.cfg &
 
@@ -112,14 +112,14 @@ Assessment of the `CHM13 <https://github.com/nanopore-wgs-consortium/CHM13>`__ g
 
 7. **Download reference**   
 
-  .. code:: console
+  .. code-block:: shell
   
     wget https://s3.amazonaws.com/nanopore-human-wgs/chm13/assemblies/chm13.draft_v0.7.fasta.gz
     gzip -d chm13.draft_v0.7.fasta.gz
 
 8. **Run Quast v5.0.2**
 
-  .. code:: console
+  .. code-block:: shell
 
     quast.py --eukaryote --large --min-identity 80 --threads 30 -r ./chm13.draft_v0.7.fasta --fragmented nd.asm.fasta
 

diff --git a/doc/TEST3.rst b/doc/TEST3.rst
@@ -7,19 +7,19 @@ Assessment of the `Arabidopsis thaliana F1 generation of Col-0 and Cvi-0 strains
 
 1. **Download reads**
 
-  .. code:: console
+  .. code-block:: shell
 
     SRA Accession: SRX1715706, SRX1715705, SRX1715704, SRX1715703
 
 2. **Prepare input file (input.fofn)**
 
-  .. code:: console
+  .. code-block:: shell
   
     ls f1.fasta.gz > input.fofn
 
 3. **Calculate the recommended minimum seed length**
 
-  .. code:: console
+  .. code-block:: shell
 
     bin/seq_stat -g 120m input.fofn > input.fofn.stat
 
@@ -48,7 +48,7 @@ Assessment of the `Arabidopsis thaliana F1 generation of Col-0 and Cvi-0 strains
 
 4. **Prepare config file (run.cfg)**
 
-  .. code:: console
+  .. code-block:: shell
 
     [General]
     job_type = sge
@@ -79,7 +79,7 @@ Assessment of the `Arabidopsis thaliana F1 generation of Col-0 and Cvi-0 strains
 
 5. **Run**   
 
-  .. code:: console
+  .. code-block:: shell
 
     nohup nextDenovo run.cfg &
 
@@ -114,19 +114,19 @@ Assessment of the `Arabidopsis thaliana F1 generation of Col-0 and Cvi-0 strains
 
 7. **Assemble with shasta** 
 
-  .. code:: console 
+  .. code-block:: shell 
     
     shasta-Linux-0.5.1 --input f1.fasta --threads 30
 
 8. **Download reference**   
 
-  .. code:: console 
+  .. code-block:: shell 
     
     wget ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas
 
 9. **Run Quast v5.0.2**
 
-  .. code:: console
+  .. code-block:: shell
   
     quast.py --large --eukaryote --min-identity 80 --threads 30 -r TAIR10_chr_all.fa nextDenovo.asm.fa Canu.asm.fa Falcon.asm.fa Flye.asm.fa Shasta.asm.fa Mecat.asm.fa Wtdbg.asm.fa
 

diff --git a/doc/TEST4.rst b/doc/TEST4.rst
@@ -7,19 +7,19 @@ Assessment of the `Drosophila melanogaster ISO1 ref. strain <https://www.ncbi.nl
 
 1. **Download reads**
 
-  .. code:: console
+  .. code-block:: shell
 
     SRA Accession: SRR6702603, SRR6821890
 
 2. **Prepare input file (input.fofn)**
 
-  .. code:: console
+  .. code-block:: shell
   
     ls SRR6702603.fasta.gz SRR6821890.fasta.gz > input.fofn
 
 3. **Calculate the recommended minimum seed length**
 
-  .. code:: console 
+  .. code-block:: shell 
 
     bin/seq_stat -g 130m input.fofn > input.fofn.stat
 
@@ -48,7 +48,7 @@ Assessment of the `Drosophila melanogaster ISO1 ref. strain <https://www.ncbi.nl
 
 4. **Prepare config file (run.cfg)**
 
-  .. code:: console
+  .. code-block:: shell
 
     [General]
     job_type = sge
@@ -79,7 +79,7 @@ Assessment of the `Drosophila melanogaster ISO1 ref. strain <https://www.ncbi.nl
 
 5. **Run**   
 
-  .. code:: console
+  .. code-block:: shell
 
     nohup nextDenovo run.cfg &
 
@@ -114,21 +114,21 @@ Assessment of the `Drosophila melanogaster ISO1 ref. strain <https://www.ncbi.nl
 
 7. **Assemble with shasta** 
 
-  .. code:: console
+  .. code-block:: shell
     
     shasta-Linux-0.5.1  --input SRR6702603.fasta --input SRR6821890.fasta --threads 30
 
 8. **Download reference**   
 
-  .. code:: console
+  .. code-block:: shell
 
     wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz
     gzip -d GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz
 
 
 9. **Run Quast v5.0.2**
 
-  .. code:: console
+  .. code-block:: shell
     
     quast.py --large --eukaryote --min-identity 80 --threads 30 -r GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna nextDenovo.asm.fa Canu.asm.fa Flye.asm.fa Shasta.asm.fa Wtdbg.asm.fa