User manual

Configuration description

1. Ancient reads as input: input_type <string>: "reads"
   reference_genome <string>: Specify the reference genome representative of a microbial species, in FASTA format. Default: "". This parameter is equivalent to --reference in the --help menu.
   age_type <int>: 1
   intermediate <string>: Specify a directory for storing intermediate files. Default: "". This parameter is equivalent to --intermediate_dir in the --help menu.
   search_report_mode <"-k,int">: The upper limit on the number of alignments Bowtie 2 should report in the search of alignments. Default: "-k,5". (The higher the value is set the more computational time required , but more accurate alignment returned.)
   bowtie2_threads <int>: Specify the thread number for bowtie2 processing each sample. Default: [1]
   minimum_mapping_quality <int>: Bases with quality score lower than the specified value will be ignored in reconstructing genome alignment. Default: [30]
   minimum_mapping_length <int>: Aligned reads with length shorter than the specified value will be ignored in reconstructing genome alignment. Default: [30]
   maximum_snp_edit_distance <float>: Reads with SNP edit distance greater the specified value will be ignored in reconstructing genome alignment. Default: [0.04]
   nproc <int>: Specify the number of processors for handling multiple samples in parallel. Default: [1]
   minimum_coverage <int>: A position with a coverage depth lower than the specified value will be ignored. Default: [5]
   trim_distance <"int:int">: The number of nucleotides to trim at two ends of ancient reads. These positions are likely damaged post-mortem. Default: "5:5"
   
   dominant_allele_frequency <float>: A position with the degree of dominant allele lower than the specified value will not be ignored in reconstructing genome alignment. Default: [0.8]
   output_trimmed_reads <int>: Specify 1 if you need to output aligned reads which are used in reconstructing genome alignment; Specify 0 if you want to skip this feature. Default: [0]
   sample <string>: Specify the directory holding ancient metagenomic reads folders. Default: "". This parameter is equivalent to --ancient_metagenomes in the --help menu.
   

2. Modern reads as input: input_type <string>: "reads"
   reference_genome <string>: Specify the reference genome representative of a microbial species, in FASTA format. This parameter is equivalent to --reference in the --help menu.
   age_type <int>: 2
   intermediate <string>: Specify a directory for storing intermediate files. Default: "". This parameter is equivalent to --intermediate_dir in the --help menu.
   search_report_mode <"-k,int">: The upper limit on the number of alignments Bowtie 2 should report in the search of alignments. Default: "-k,5". (The higher the value is set the more computational time required , but more accurate alignment returned)
   bowtie2_threads <int>: Specify the thread number for bowtie2 processing each sample. Default: [1]
   minimum_mapping_quality <int>: Bases with quality score lower than the specified value will be ignored in reconstructing genome alignment. Default: [30]
   minimum_mapping_length <int>: Aligned reads with length shorter than the specified value will be ignored in reconstructing genome alignment. Default: [30]
   maximum_snp_edit_distance <float>: Reads with SNP edit distance greater the specified value will be ignored in reconstructing genome alignment. Default: [0.04]
   nproc <int>: Specify the number of processors for handling multiple samples in parallel. Default: [1]
   minimum_coverage <int>: A position with a coverage depth lower than the specified value will be ignored. Default: [5]
   dominant_allele_frequency <float>: A position with the degree of dominant allele lower than the specified value will not be ignored in reconstructing genome alignment. Default: [0.8]
   sample <string>: Specify the directory holding modern metagenomic reads folders. Default: "". This parameter is equivalent to --modern_metagenomes in the --help menu.
   

3. Assembled contigs as input: input_type: "contigs"
   reference_genome: Specify the reference genome representative of a microbial species, in FASTA format. This parameter is equivalent to --reference in the --help menu.
   intermediate: Specify a directory for storing intermediate files. Default: "". This parameter is equivalent to --intermediate_dir in the --help menu.
   homolog_length <int>: The minimum length for the aligned part of a contig to be considered as a homolog in order to be used in reconstructing genome alignment. Default: [500]
   
   homolog_indentity <float>:The minimum identity for the aligned part of a contig to be considered as a homolog in order to be used in reconstructing genome alignment. Default: [95.0]
   
   blastn_threads <int>: Specify the number of threads used for blastn.
   sample <string>: Specify the directory holding assembled contigs files. Default: "". This parameter is equivalent to --genome_assemblies in the --help menu.