diff --git a/README.md b/README.md index 80873ec..2d9bf65 100644 --- 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/). \ No newline at end of file +The complete user documentation is available [here](https://nextdenovo.readthedocs.io/en/latest/). diff --git a/doc/OPTION.rst b/doc/OPTION.rst index 570d2ad..074af95 100644 --- 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 ` for details. \ No newline at end of file + nextgraph options, see :ref:`nextgraph ` for details. diff --git a/doc/QSTART.rst b/doc/QSTART.rst index e9596c1..0aa2c9c 100644 --- 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 `__ 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 @@ -79,12 +82,12 @@ 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 ./ @@ -92,7 +95,7 @@ Quick Start #. 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 `_. +You can track updates by tab the ``Star`` button on the upper-right corner at the `github page `_. .. |ss| raw:: html diff --git a/doc/TEST1.rst b/doc/TEST1.rst index d9c2f8c..e3d1f09 100644 --- 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 index 09607b5..500c904 100644 --- a/doc/TEST2.rst +++ b/doc/TEST2.rst @@ -7,19 +7,19 @@ Assessment of the `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 `__ g 4. **Prepare config file (run.cfg)** - .. code:: console + .. code-block:: shell [General] job_type = sge @@ -78,7 +78,7 @@ Assessment of the `CHM13 `__ g 5. **Run** - .. code:: console + .. code-block:: shell nohup nextDenovo run.cfg & @@ -112,14 +112,14 @@ Assessment of the `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 index a309043..3f862f3 100644 --- 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 index 75ba01e..cf2c3cb 100644 --- a/doc/TEST4.rst +++ b/doc/TEST4.rst @@ -7,19 +7,19 @@ Assessment of the `Drosophila melanogaster ISO1 ref. strain 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