Reference

Generate the folders

build_stackr_workflow_dir()

Build stacks 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_reads()

Summarise the reads for indel and GC content and produce the read depth plot

summary_sstacks()

Summarize STACKS sstacks log file generated by stackr

summary_ustacks()

Summarize STACKS ustacks files

Utility functions

read_depth_plot()

Generate a figure with the read depth groups

reads_length_distribution()

Generate the read length distribution of a fastq file

clean_fq()

Removes the noise of an individual fastq file

read_counter()

Counts the number of reads in samples

normalize_reads()

Rarefaction of reads samples

rename_fq()

Rename fastq files

extract_catalog_sql_ids()

Extract sample SQL IDs from STACKS catalog file