Hook in syntax highlighter. Remove extra newlines

docs/datatypes.md

@@ -31,14 +31,12 @@ We recommend that you check the SPAdes log file at the end of the each iteration
 For reads corrected prior to running the assembler:
 
 ``` bash
-
     spades.py -k 21,33,55,77 --careful --only-assembler <your reads> -o spades_output
 ```
 
 To correct and assemble the reads:
 
 ``` bash
-
     spades.py -k 21,33,55,77 --careful <your reads> -o spades_output
 ```
 
@@ -55,14 +53,12 @@ We recommend you to check the SPAdes log file at the end of each iteration to co
 For reads corrected prior to running the assembler:
 
 ``` bash
-
     spades.py -k 21,33,55,77,99,127 --careful --only-assembler <your reads> -o spades_output
 ```
 
 To correct and assemble the reads:
 
 ``` bash
-
     spades.py -k 21,33,55,77,99,127 --careful <your reads> -o spades_output
 ```
 

docs/getting-started.md

@@ -6,36 +6,36 @@
 
 - Test your SPAdes installation by running
 
-```
+``` bash
     bin/spades.py --test
 ```
 
 - A single paired-end library (separate files, gzipped):
 
-```
+``` bash
     bin/spades.py -1 left.fastq.gz -2 right.fastq.gz -o output_folder
 ```
 
 - A single paired-end library (interlaced reads):
 
-```
+``` bash
     bin/spades.py --12 interlaced.fastq -o output_folder
 ```
 
 - Two paired-end libraries (separate files):
 
-```
+``` bash
     bin/spades.py --pe1-1 1_left.fastq --pe1-2 1_right.fastq --pe2-1 2_left.fastq --pe2-2 2_right.fastq -o output_folder
 ```
 
 - IonTorrent data:
-```
+``` bash
     bin/spades.py --iontorrent -s it_reads.fastq -o output_folder
 ```
 
 - A paired-end library coupled with long PacBio reads:
 
-```
+``` bash
     bin/spades.py -1 left.fastq.gz -2 right.fastq.gz --pacbio pb.fastq -o output_folder
 ```
 

docs/installation.md

@@ -28,7 +28,6 @@ In case of successful installation the following files will be placed in the `bi
 To download [SPAdes Linux binaries](https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Linux.tar.gz) and extract them, go to the directory in which you wish SPAdes to be installed and run:
 
 ``` bash
-
     wget https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Linux.tar.gz
     tar -xzf SPAdes-3.15.5-Linux.tar.gz
     cd SPAdes-3.15.5-Linux/bin/
@@ -44,7 +43,6 @@ Note, that pre-build binaries do not work on new Linux kernels.
 To obtain [SPAdes binaries for Mac](https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Darwin.tar.gz), go to the directory in which you wish SPAdes to be installed and run:
 
 ``` bash
-
     curl https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Darwin.tar.gz
     tar -zxf SPAdes-3.15.5-Darwin.tar.gz
     cd SPAdes-3.15.5-Darwin/bin/
@@ -65,7 +63,6 @@ If you wish to compile SPAdes by yourself you will need the following libraries
 If you meet these requirements, you can download the [SPAdes source code](https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5.tar.gz):
 
 ``` bash
-
     wget https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5.tar.gz
     tar -xzf SPAdes-3.15.5.tar.gz
     cd SPAdes-3.15.5
@@ -74,21 +71,18 @@ If you meet these requirements, you can download the [SPAdes source code](https:
 and build it with the following script:
 
 ``` bash
-
     ./spades_compile.sh
 ```
 
 SPAdes will be built in the directory `./bin`. If you wish to install SPAdes into another directory, you can specify full path of destination folder by running the following command in `bash` or `sh`:
 
 ``` bash
-
     PREFIX=<destination_dir> ./spades_compile.sh
 ```
 
 for example:
 
 ``` bash
-
     PREFIX=/usr/local ./spades_compile.sh
 ```
 
@@ -102,14 +96,12 @@ After installation you will get the same files (listed above) in `./bin` directo
 For testing purposes, SPAdes comes with a toy data set (reads that align to first 1000 bp of *E. coli*). To try SPAdes on this data set, run:
 
 ``` bash
-
     <spades installation dir>/bin/spades.py --test
 ```
 
 If you added `bin` folder from SPAdes installation directory to the `PATH` variable, you can run:
 
 ``` bash
-
     spades.py --test
 ```
 
@@ -118,7 +110,6 @@ For simplicity we further assume that the `bin` folder from SPAdes installation
 If the installation is successful, you will find the following information at the end of the log:
 
 ``` plain
-
 ===== Assembling finished. Used k-mer sizes: 21, 33, 55
 
  * Corrected reads are in spades_test/corrected/

docs/running.md

@@ -3,7 +3,6 @@
 To run SPAdes from the command line, type
 
 ``` bash
-
     spades.py [options] -o <output_dir>
 ```
 
@@ -238,8 +237,7 @@ The value for each attribute is given after a colon. Comma-separated lists of fi
 
 For example, if you have one paired-end library split into two pairs of files:
 
-``` bash
-
+``` plain
     lib_pe1_left_1.fastq
     lib_pe1_right_1.fastq
     lib_pe1_left_2.fastq
@@ -248,24 +246,21 @@ For example, if you have one paired-end library split into two pairs of files:
 
 one mate-pair library:
 
-``` bash
-
+``` plain
     lib_mp1_left.fastq
     lib_mp1_right.fastq
 ```
 
 and PacBio CCS and CLR reads:
 
-``` bash
-
+``` plain
     pacbio_ccs.fastq
     pacbio_clr.fastq
 ```
 
 YAML file should look like this:
 
-``` bash
-
+``` yaml
     [
       {
         orientation: "fr",
@@ -342,15 +337,13 @@ Notes:
 To test the toy data set, you can also run the following command from the SPAdes `bin` directory:
 
 ``` bash
-
     spades.py --pe1-1 ../share/spades/test_dataset/ecoli_1K_1.fq.gz \
     --pe1-2 ../share/spades/test_dataset/ecoli_1K_2.fq.gz -o spades_test
 ```
 
 If you have your library separated into several pairs of files, for example:
 
-``` bash
-
+``` plain
     lib1_forward_1.fastq
     lib1_reverse_1.fastq
     lib1_forward_2.fastq
@@ -360,7 +353,6 @@ If you have your library separated into several pairs of files, for example:
 make sure that corresponding files are given in the same order:
 
 ``` bash
-
     spades.py --pe1-1 lib1_forward_1.fastq --pe1-2 lib1_reverse_1.fastq \
     --pe1-1 lib1_forward_2.fastq --pe1-2 lib1_reverse_2.fastq \
     -o spades_output
@@ -369,7 +361,6 @@ make sure that corresponding files are given in the same order:
 Files with interlacing paired-end reads or files with unpaired reads can be specified in any order with one file per option, for example:
 
 ``` bash
-
     spades.py --pe1-12 lib1_1.fastq --pe1-12 lib1_2.fastq \
     --pe1-s lib1_unpaired_1.fastq --pe1-s lib1_unpaired_2.fastq \
     -o spades_output
@@ -379,32 +370,28 @@ If you have several paired-end and mate-pair reads, for example:
 
 paired-end library 1
 
-``` bash
-
+``` plain
     lib_pe1_left.fastq
     lib_pe1_right.fastq
 ```
 
 mate-pair library 1
 
-``` bash
-
+``` plain
     lib_mp1_left.fastq
     lib_mp1_right.fastq
 ```
 
 mate-pair library 2
 
-``` bash
-
+``` plain
     lib_mp2_left.fastq
     lib_mp2_right.fastq
 ```
 
 make sure that files corresponding to each library are grouped together:
 
 ``` bash
-
     spades.py --pe1-1 lib_pe1_left.fastq --pe1-2 lib_pe1_right.fastq \
     --mp1-1 lib_mp1_left.fastq --mp1-2 lib_mp1_right.fastq \
     --mp2-1 lib_mp2_left.fastq --mp2-2 lib_mp2_right.fastq \
@@ -413,8 +400,7 @@ make sure that files corresponding to each library are grouped together:
 
 If you have IonTorrent unpaired reads, PacBio CLR and additional reliable contigs:
 
-``` bash
-
+``` plain
     it_reads.fastq
     pacbio_clr.fastq
     contigs.fasta
@@ -423,16 +409,14 @@ If you have IonTorrent unpaired reads, PacBio CLR and additional reliable contig
 run SPAdes with the following command:
 
 ``` bash
-
     spades.py --iontorrent -s it_reads.fastq \
     --pacbio pacbio_clr.fastq --trusted-contigs contigs.fastq \
     -o spades_output
 ```
 
 If a single-read library is split into several files:
 
-``` bash
-
+``` plain
     unpaired1_1.fastq
     unpaired1_2.fastq
     unpaired1_3.fasta
@@ -441,7 +425,6 @@ If a single-read library is split into several files:
 specify them as one library:
 
 ``` bash
-
     spades.py --s1 unpaired1_1.fastq \
     --s1 unpaired1_2.fastq --s1 unpaired1_3.fastq \
     -o spades_output

docs/standalone.md

@@ -14,7 +14,7 @@ Example:
         For k-mer: AGCTCT
         Memory: 6 bits * 2 = 12, 64 bits (8 bytes)
         Let’s describe bytes:
-        data[0] = AGCT -> 11 01 10 00 -> 0xd8                              
+        data[0] = AGCT -> 11 01 10 00 -> 0xd8
         data[1] = CT00 -> 00 00 11 01 -> 0x0d
         data[2] = 0000 -> 00 00 00 00 -> 0x00
         data[3] = 0000 -> 00 00 00 00 -> 0x00

mkdocs.yml

@@ -1,9 +1,10 @@
 site_name: SPAdes Assembly Toolkit
+
 nav:
   - Home: index.md
   - Quick start: getting-started.md
   - Installation: installation.md
-  - SPAdes input data: 
+  - SPAdes input data:
     - Basic input: input.md
     - Hybrid assembly: hybrid.md
     - Tips on the parameters: datatypes.md
@@ -14,5 +15,20 @@ nav:
   - SPAdes tools: standalone.md
   - Citation: citation.md
   - Feedback: feedback.md
-theme: material
+
 use_directory_urls: false
+
+theme:
+  name: material
+  features:
+    - content.code.copy
+
+markdown_extensions:
+  - pymdownx.highlight:
+      use_pygments: true
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences