------- ipyrad params file (v.0.9.81)-------------------------------------------
CIR-HYB                        ## [0] [assembly_name] pojmenovani pocatecni zkratky vsech vystupu (output); soucasne nazev pro params file
./                             ## [1] [project_dir]: umisteni projektu; cesta k souboru params file
                               ## [2] [raw_fastq_path]: Location of raw non-demultiplexed fastq files
                 	       ## [3] [barcodes_path]: Location of barcodes file
./*.fastq.gz                   ## [4] [sorted_fastq_path]: Location of demultiplexed/sorted fastq files
denovo                         ## [5] [assembly_method]: Assembly method (denovo, reference)
                               ## [6] [reference_sequence]: Location of reference sequence file
rad                            ## [7] [datatype]: Datatype (see docs): rad, gbs, ddrad, etc.
TGCAG                          ## [8] [restriction_overhang]: Restriction overhang (cut1,) or (cut1, cut2)
5                              ## [9] [max_low_qual_bases]: Max low quality base calls (Q<20) in a read; DEFOLT=5
33                             ## [10] [phred_Qscore_offset]: phred Q score offset (33 is default and very standard)
6                              ## [11] [mindepth_statistical]: MIN POCET STEJNYCH SEKVENCI (STACKS=m); 6=DEFOLT
6                              ## [12] [mindepth_majrule]: KDYZ JE MALO A RUZNYCH SEKVENCI, TAK VYBERE MAJORITNI MOTIV
10000                          ## [13] [maxdepth]: Max cluster depth within samples; OMEZENI REPETIC
0.90   			       ## [14] [clust_threshold]: Clustering threshold: PODOBNOST DVOU SEKVENCI, ABY BYLY STALE JEDEN LOKUS      
0 		               ## [15] [max_barcode_mismatch]: Max number of allowable mismatches in barcodes
1                              ## [16] [filter_adapters]: Filter for adapters/primers (1 or 2=stricter);PROBLEM GBS+ddRADů; 0=NERESIT; 1=RESIT DLE KVALITY
70                             ## [17] [filter_min_trim_len]: Min length of reads after adapter trim; POKUD V BODU16 1 NEBO 2, PAK ZDE STANOVÝM JAKÁ MUSÍ BÝT MINIMÁLNÍ SEKVENCE PO OŘEZECH.
2 		               ## [18] [max_alleles_consens]: Max alleles per site in consensus sequences; POCET ALEL V LOKUSU
0.05                           ## [19] [max_Ns_consens]: Max N's (uncalled bases) in consensus; PROCENTICKE ZASTOUPENI N BAZI V KONSENZUALNI SEKV.
0.05 			       ## [20] [max_Hs_consens]: KOLIK PROCENT MIST SE V KONSENZUALNI SEKV. MŮŽE LIŠIT (ROZDILNE BAZE) (STACKS=M)
3   			       ## [21] [min_samples_locus]: Min # samples per locus for output; KOLIK VZORKU/JEDINCŮ MUSI MIT UDAJ V LOKUSU
0.2                            ## [22] [max_SNPs_locus]: Max # SNPs per locus; KOLIK PROCENT SNP MUZE BYT V LOKUSU
8                              ## [23] [max_Indels_locus]: Max # of indels per locus
0.5                            ## [24] [max_shared_Hs_locus]: Max # heterozygous sites per locus; OCHRANA PROTI PARALOGŮM (DEFOLT=0.5)
0, 0, 0, 0                     ## [25] [trim_reads]: Trim raw read edges (R1>, <R1, R2>, <R2) (see docs); MOZNOST OREZU PRI PROBLEMOVYCH DATECH
0, 0, 0, 0                     ## [26] [trim_loci]: Trim locus edges (see docs) (R1>, <R1, R2>, <R2); MOZNOST OREZU PO ALIGNMENTU; UZITECNE
*                              ## [27] [output_formats]: Output formats (see docs); *=VYTVORI SE VSECHNY OUTPUT SOUBORY
                               ## [28] [pop_assign_file]: Path to population assignment file; CESTA K POPULACNIM DATUP: soubor.txt 
                               ## [29] [reference_as_filter]: Reads mapped to this reference are removed in step 3