grch38_essential.fa reference file needs to be loaded in </path/to/references/directory>, indexed by BWA and SequenceDictionary generated by picard tools.
GRCh38 reference file needs to be loaded in </path/to/references/directory>, decompressed, indexed by BWA and SequenceDictionary generated by picard tools. The GRCh38 genome version is mandatory (you can not use hg19). You can download it from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
samples.R1.fastq.gz and sample.R2.fastq.gz files need to be loaded in <path/to/fastq/gz/samples/files/directory> without folder. Each sample needs to be sequenced in paired-end.
samples.R1.fastq.gz and sample.R2.fastq.gz files need to be loaded in <path/to/fastq/gz/samples/files/directory> without subfolder. Each sample needs to be sequenced in paired-end.
## Hardware requirements
We strongly recommend a computer with at least:
- Memory 16 Go.
- CPU 2 to 16 cores.
- 30 Go disk space.
## Download Pipeline
## Download Pipeline
We provide a docker version for local usage. Download docker image pipelinemitov1.tar (https://ADRESSE)
We provide a docker version for local usage. Download docker image pipelinemitov1.tar (http://gitlab.gad-bioinfo.org/gad-public/pipelinemito)
## Load and run pipeline
## Load and run pipeline
Commands:
Commands:
docker load -i pipelinemitov1.tar
docker load -i pipelinemitov1.tar
docker run -v /path/to/fastq/gz/samples/files/directory:/data:rw -v /path/to/references/directory:/mitopipeline:ro --env THREAD=<int> pipelinemitov1
