Reference

Generate the folders

build_stackr_workflow_dir()

Automatically build the stacks/stackr workflow directories

run_process_radtags()

Run STACKS process_radtags module

run_ustacks()

Run STACKS ustacks module

run_cstacks()

Run STACKS cstacks module

run_sstacks()

Run STACKS sstacks module

run_tsv2bam()

Run STACKS tsv2bam and merges BAM files

run_gstacks()

Run STACKS new module called gstacks

run_populations()

Run STACKS Version >= 2.0 populations module

stacks ustacks-cstacks alternative function

run_radproc()

Run RADproc

Summary functions

summary_catalog_log_lik()

Summary of catalog log likelihood

summary_cstacks()

Summarize STACKS cstacks log file generated by stackr

summary_genotypes()

Summary of batch_x.genotypes.txt and batch_x.markers.tsv files.

summary_haplotypes()

Haplotypes file summary

summary_pstacks()

Summarize STACKS pstacks files

summary_sstacks()

Summarize STACKS sstacks log file generated by stackr

summary_ustacks()

Summarize STACKS ustacks files

Utility functions

rename_fq()

Rename fastq files

extract_catalog_sql_ids()

Extract sample SQL IDs from STACKS catalog file