Table 2 Catalog of pre-built data recipes in ReUseData
From: ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management
ReUseData recipes | Description |
|---|---|
bowtie2_index | Use "bowtie2-build" to index a specific reference genome |
echo_out | Print a character string and output as a txt file |
ensembl_liftover | Download and unzip genome liftover file from Ensembl |
gcp_broad_gatk_hg19 | Download file in GATK annotation bundle for hg19 from GCP |
gcp_broad_gatk_hg38 | Download file in GATK annotation bundle for hg38 from GCP |
gcp_gatk_mutect2_b37 | Download file in GATK mutect2 bundle for b37 from GCP |
gcp_gatk_mutect2_hg38 | Download file in GATK mutect2 bundle for hg38 from GCP |
gencode_annotation | Download and unzip annotation files from gencode |
gencode_genome_grch38 | Download human genome GRCh38 from GENCODE release 42 |
gencode_transcripts | Download, unzip, and index transcripts files from gencode |
hisat2_index | Use "hisat2-build" to build the index files |
reference_genome | Download, format and index reference genome file with samtools, picard and bwa |
salmon_index | Use "Salmon index" command to build salmon index for your transcriptome |
STAR_index | Use STAR command to build genome index for STAR alignment |
ucsc_database | Download genome annotation file from UCSC database using the golden path |