Table of Contents
Use precomputed edit distance read variants to assign reads to references. This process is commonly referred to as barcode matching. Palmer works by precomputing the user specified k-error variants of a reference and storing them in a hash map of <variant ⇒ reference>. Then, for each input read, looks up the read sequence in this table and maps them to the appropriate reference if they fall within the k-error budget.
Palmer supports one-pass and two-pass fixed reference start oligo reads.
Generic options:
--help produce help message
--version produce version message
--reference_file_pass1 arg first pass reference FASTA file name
Required options:
--read_file arg read file name
--flow_cells arg (=1-2) flowcells to process
--channels arg (=1-25) channels to process
--hits arg (=hits.csv) filename for count output
Optional options:
--reference_file_pass2 arg second pass reference FASTA file name
--max_errors_pass1 arg (=0) first pass error budget
--max_errors_pass2 arg (=0) second pass error budget
--spikes arg filename for spike reads output
--discards arg filename for discarded reads output
--discard_length arg (=6) minimum discard read length
--split_hits arg (=0) split hits into distinct sms files after trimming
barcode prefix
--spacer_char arg nucleotide spacer found between a sample barcode
and the sample read
--allow_del arg (=1) allow deletions in matches
--allow_sub arg (=1) allow substitutions in matches
--allow_ins arg (=1) allow insertions in matches
--hits_pass1 arg filename for count output from pass 1 of a 2 pass
read
--hits_pass2 arg filename for count output from pass 2 of a 2 pass
read
--prefix arg Prefix for output files