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Functions
- branch_and_search()
- calculate_percent()
- calculate_simpson()
- calculate_variant_within_group()
- cal_fn()
- cal_fp()
- cal_met_snp()
- check_fasta_meta_mapping()
- check_multistate()
- check_percent()
- combine_fastq_search_result()
- combine_search_string_result()
- combine_search_string_result_from_files()
- combine_search_string_result_from_list()
- estimate_coverage()
- extend_length()
- find_optimised_snps()
- flag_allele()
- flag_position()
- full_merge()
- full_merge_1()
- generate_kmers()
- generate_kmer_search_string()
- generate_pattern()
- generate_snp_search_string()
- get_all_process_methods()
- get_metric_fun()
- get_positions_to_search()
- get_snps_set()
- get_usual_length()
- identify_overlaps()
- infer_from_combined()
- iterate_merge()
- iterate_through()
- match_count()
- merge_fasta()
- output_parsed()
- output_result()
- output_to_files()
- process_allele()
- process_kmer_result()
- process_result_file()
- process_snp_result()
- read_fasta()
- read_sequences_from_fastq()
- remove_dup_isolate()
- remove_snp_conflict()
- resolve_IUPAC_missing()
- reverse_complement()
- search_from_fastq_reads()
- select_n_set_i_depth()
- sequence_reads_match_count()
- view_percent()
- view_simpson()
- write_fasta()
R Codes
Selected R package: minSNPs
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