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.