Index

Symbols

--cutadapt <adapter_file> <search_options> command line option --db_16S <database> command line option --db_ITS <database> command line option --db_NCBI_taxonomy command line option --db_reconstruct command line option --db_refseq_fungi <databases> command line option --db_refseq_plant command line option --db_taxonomy_16S command line option --db_taxonomy_ITS command line option --ins_len <insert_length> command line option -16S command line option -e command line option -h, --help command line option

-humann command line option -ic <method>, --initial_cleaning <method> command line option -ITS command line option -m <mode>, --mode <mode> command line option -MV <parameters> command line option -o <output_directory>, --out_dir <output_directory> command line option -ot <output_type_list>, --output_type <output_type_list> command line option -postfix <postfix> command line option -r <root_directory>, --root_dir <root_directory> command line option -rapsearch <database> command line option -reconstruct <option> command line option -refseq <kingdom> command line option -t <threads>, --threads <threads> command line option

A

adapter_read() (in module refseq_bipype) adapter_read_bck() (in module refseq_bipype)

auto_tax_read() (in module metatranscriptomics_bipype) (in module refseq_bipype)

B

bam_idxstating() (in module refseq_bipype) bam_indexing() (in module refseq_bipype) bam_make() (in module refseq_bipype)

bam_sorting() (in module refseq_bipype) bipype (module) bowtie2_run() (in module refseq_bipype)

C

cat_read() (in module refseq_bipype) command line option --cutadapt <adapter_file> <search_options> --db_16S <database> --db_ITS <database> --db_NCBI_taxonomy --db_reconstruct --db_refseq_fungi <databases> --db_refseq_plant --db_taxonomy_16S --db_taxonomy_ITS --ins_len <insert_length> -16S -ITS -MV <parameters> -e -h, --help -humann -ic <method>, --initial_cleaning <method> -m <mode>, --mode <mode> -o <output_directory>, --out_dir <output_directory> -ot <output_type_list>, --output_type <output_type_list> -postfix <postfix> -r <root_directory>, --root_dir <root_directory> -rapsearch <database> -reconstruct <option> -refseq <kingdom> -t <threads>, --threads <threads> config_from_file() (in module metatranscriptomics_bipype) connect_db() (in module metatranscriptomics_bipype)

create_krona_html() (in module refseq_bipype) create_krona_xml() (in module refseq_bipype) cutadapt() (in module refseq_bipype)

D

deunique() (in module refseq_bipype) dict_prepare() (in module refseq_bipype) dict_purify() (in module refseq_bipype)

dict_sum() (in module refseq_bipype) dicto_reduce() (in module metatranscriptomics_bipype)

E

exist_check() (in module refseq_bipype)

F

fastq_dict() (in module refseq_bipype) fastq_to_fasta() (in module metatranscriptomics_bipype)

file_analysis() (in module refseq_bipype)

G

get_kegg_name() (in module metatranscriptomics_bipype) get_ko_fc() (in module metatranscriptomics_bipype) get_kopathways() (in module metatranscriptomics_bipype) get_pathways() (in module metatranscriptomics_bipype)

get_tables() (in module metatranscriptomics_bipype) graphlan_to_krona() (in module refseq_bipype) gzip_MV() (in module refseq_bipype)

H

humann() (in module refseq_bipype)

I

idx_map() (in module refseq_bipype) idx_reader() (in module refseq_bipype) idxstat_perling() (in module refseq_bipype)

input_locations() (in module refseq_bipype) ins_len_read() (in module refseq_bipype)

L

linia_unique() (in module refseq_bipype)

low_change() (in module metatranscriptomics_bipype)

M

m8_to_ko() (in module metatranscriptomics_bipype) mapper() (in module metatranscriptomics_bipype) mapper_write() (in module metatranscriptomics_bipype) metatranscriptomics() (in module metatranscriptomics_bipype)

metatranscriptomics_bipype (module) MH() (in module refseq_bipype) MV() (in module refseq_bipype)

N

name_total_reduction() (in module refseq_bipype)

O

out_content() (in module metatranscriptomics_bipype)

out_namespace() (in module refseq_bipype)

P

pair_uni_name() (in module refseq_bipype) paired_end_match() (in module refseq_bipype) parse_arguments() (in module bipype) pickle_or_db() (in module metatranscriptomics_bipype)

prepare_taxonomy_dicts() (in module refseq_bipype) prepare_taxonomy_stats() (in module refseq_bipype) prettify() (in module refseq_bipype) progress() (in module metatranscriptomics_bipype)

R

rapsearch() (in module refseq_bipype) rapsearch2() (in module metatranscriptomics_bipype) reconstruct() (in module refseq_bipype) refseq_bipype (module) refseq_mapping() (in module refseq_bipype) refseq_ref_namespace() (in module refseq_bipype) run_cat_pairing() (in module metatranscriptomics_bipype) run_fastq_to_fasta() (in module metatranscriptomics_bipype)

run_ko_csv() (in module metatranscriptomics_bipype) run_ko_map() (in module metatranscriptomics_bipype) run_ko_remap() (in module metatranscriptomics_bipype) run_megan() (in module refseq_bipype) run_new_ko_remap() (in module metatranscriptomics_bipype) run_pre_ko_remap() (in module metatranscriptomics_bipype) run_rapsearch() (in module metatranscriptomics_bipype) run_SARTools() (in module metatranscriptomics_bipype)

S

sam_merge() (in module refseq_bipype) sample() (in module refseq_bipype)

SSU_read() (in module refseq_bipype)

T

tax_id_reader() (in module refseq_bipype) tax_name_reader() (in module refseq_bipype) tax_tree_extend() (in module refseq_bipype) tax_tree_graphlan() (in module refseq_bipype) taxa_read() (in module refseq_bipype)

tree_of_life() (in module refseq_bipype) tuple_to_dict() (in module refseq_bipype) tuple_to_xml_dict() (in module refseq_bipype) txt_dict_clean() (in module refseq_bipype)

U

update_dict() (in module refseq_bipype)

usearch() (in module refseq_bipype)

X

xml_counts_graphlan() (in module refseq_bipype) xml_format() (in module refseq_bipype) xml_name_parse() (in module refseq_bipype)

xml_names_graphlan() (in module refseq_bipype) xml_prepare() (in module refseq_bipype) xml_vals() (in module refseq_bipype)