add_allele_no           add allele_no to genotypes
amplisas2tidy           Read AmpliSAT results into tidy variants
check1_lowcount         Check1
check2_unique_snames    Check2
check3_non_orphan       Check3
check_raw_reads         Check input raw FASTA/Q files
compare_calls           Comparision between multiple tidy variants or
                        genotypes.
cutadapt_command        Create cutadapt command
demultiplex             Demultiplex reads by locus
dereplicate             De-replicate reads into frequency tables for a
                        set of FASTQ files
dist_m                  Distance between two matrices
dist_m_all              Applies distance between all tables in a list.
explore_dada            Explore variants output by DADA2 in the
                        parameter space
filter_variants         Filter variants based on frequency and depth
genotype                Genotype samples from tidy variants
genotype_conversion     Conversion among genotype formats: tidy,
                        compact, wide, STRUCTURE
genotypes               Genotypes
mds_comp                plot MDS
out_popart              Format MSA and traits for PopArt
primers                 Primers for multiplex PCR
reads_loci_samples      Output reads per locus
reads_track             Output reads across pipeline
remove_hemizygotes      Remove hemizygote calls
remove_monomorphic      Remove monorphic loci
remove_poor_fastq       Remove empty FASTQ
rename_alleles          Rename alleles in a dataframe based on
                        reference alleles
rm_n_msa                Remove Ns introduced in
                        'mergePairs(justConcatenate = T)'
tidy2sequences          Output FASTA sequences
trunc_fr                Per-locus truncation lengths for forward and
                        reverse reads.
truncate                Truncate reads
var_seq2len             Convert sequence-based variants to length-based
variant_call            Variant calling
variant_calling_dada    Variant calling using DADA2 ASV approach
variant_calls           List of tidy variants
variants                Variants
