README.md

mitology-pipeline

Pipeline for plant organites (chloroplast and mitochondrion) assembly

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Dependencies

The following dependencies need to be installed manually:

• bash-common
• log4sh

The following dependencies can be installed using conda (recommended):

• bgzip
• bwa
• bcftools
• khmer
• MetaVelvet
• Velvet
• nucmer
• quast
• samtools
• tabix

install bash-common

Clone the bash-common repository then install the bash library (tag: mitology) system-wide into /usr/local under share directory (need to have at least sudoer privileges):

git clone https://github.com/jos4uke/bash-common.git 
cd bash-common
sudo bash install.sh mitology /usr/local

install log4sh

Clone the log4sh repository into /usr/loca/share (need at least to have sudoer privileges):

cd /usr/local/share
sudo git clone https://github.com/kward/log4sh.git

Installation

cd /usr/local/share
sudo git clone https://github.com/jos4uke/mitology-pipeline.git
cd mitology-pipeline

File content

# tree
├── bin     # contains the main pipeline script
│   └── mitology-pipeline.sh
├── COPYING
├── README.md
└── share   # contains the main pipeline script
    └── mitology-pipeline
        ├── etc     # contains the pipeline configuration file to be copied by the end user
        │   └── mitology-pipeline_user.config
        ├── lib     # contains specific bash library functions
        │   ├── mitology-alignments_lib.inc
        │   └── mitology-pipeline_lib.inc
        └── scripts     # helper scripts
            ├── plot_hashcount.sh
            ├── R
            │   ├── length-weigthed_kmer_coverage_hist.rplot.R
            │   └── plot_hashcount_hist.R
            ├── run_meta-velvetg.sh
            └── split_files.sh

7 directories, 12 files

Usage guide

Steps:

1. get a copy of the configuration file
2. update the configuration file
3. run the pipeline

get a copy of the configuration file

cp share/mitology-pipeline/etc/mitology-pipeline_user.config .

update the configuration file

The configuration file contains different sections:

• paths
• genome_alias
• sample
• khmer_load_into_counting
• khmer_filter_abund
• contig_assembler
• scaffolder
• velveth
• velvetg
• meta_velvetg
• quast
• bwa_aln
• bwa_sampe
• filtering
• samtools_view
• samtools_mpileup
• bcftools_view
• bgzip

In the [paths] section, you need to update path to all resources listed as <key>=<value> pair.

• GENOMES_BASE_PATH and INDEXES_BASE_PATH are the root directory path to genomes files and tool index respectively.
• BWA_INDEXES and SAMTOOLS_INDEXES are the location of the bwa and samtools indexes directories respectively.
• bcftools, bgzip, bwa, khmer_*, etc. are the paths to the corresponding tools. They should be reachable from your PATH else please indicate the absolute path. It is recommended to install all these tools using conda.

In the [genome_alias], you need to update all prefixes/aliases to reference genomes used notably for indexes listed as <key>=<value> pair. ref and ref_short aliases refer to the host genome, whereas ref_mito* and ref_chloro* aliases refer to the mitochondrial and chloroplast genomes or annotations (gff) respectively.

In the [sample] section, you need to update the sample alias and paths listed as <key>=<value> pair. name_alias will be used to identify sample in the pipeline. And seqfile_parent_dir is the parent directory location of the paired-end reads files specified by seqfile_{R1,R2} keys.

The other sections refer to options specific to pipeline steps and tools, listed again as <key>=<value> pair. Please refer to the tool documentation to update the options values.

run the pipeline

Run the pipeline using the updated config file, and output results into results directory.

bash bin/mitology-pipeline.sh -c mitology-pipeline_user.config -o results 

Please checkout the usage help with bash mitology-pipeline.sh --help

ouput files

todo:

• describe here all output files
• need some test dataset

Authors

• @jos4uke

Acknowledgements

IJPB Bioinformatics team

License

see COPYING