Files in chutter/MitoCap
Package For extracting, assembling, annotating and aligning mitochondrial genomes from high-throughput sequencing data
.Rbuildignore
.gitignore
DESCRIPTION
MitoTrawlR.Rproj
NAMESPACE
R/alignMitogenomes.R
R/annotateMitoContigs.R
R/barcodeSampleScan.R
R/buildMitogenomes.R
R/buildReference.R
R/findORF.R
R/isCircularGenome.R
R/iterativeAssemble.R
R/markerAlignment.R
R/mitochondrialCapture.R
R/prepareAlignments.R
R/readGenbank.R
R/removeOffTarget.R
R/runCap3.R
R/runSpades.R
R/setupCheck.R
R/tRNAscan.R
R/tRNAscanBatch.R
R/trimMitoAlignments.R
README.md
man/alignMitogenomes.Rd
man/annotateMitoContigs.Rd
man/buildMitogenomes.Rd
man/findORF.Rd
man/isCircularGenome.Rd
man/iterativeAssemble.Rd
man/makeReference.Rd
man/markerAlignment.Rd
man/mitochondrialCapture.Rd
man/prepareAlignments.Rd
man/removeOffTarget.Rd
man/runCap3.Rd
man/tRNAscan.Rd
man/tRNAscanBatch.Rd
man/trimMitoAlignments.Rd
setup-configuration_files/Example_pbs_job.sh
setup-configuration_files/bash_manual-install_mitocap-advanced.sh
setup-configuration_files/configuration-file.R
setup-configuration_files/environment.yml
setup-configuration_files/mitoGenome-workflow.R
