package bistro-bio

You can search for identifiers within the package.

in-package search v0.2.0

bistro-bio
- Bistro_bio
  - Alignment_stats
  - Bed
  - Bedtools
    
    Cmd
  - Bowtie
  - Bowtie2
  - Busco
  - ChIPQC
  - Cisa
  - Cisbp
  - Comparative_genomics
  - DESeq2
    
    table
  - Deeptools
    
    compressed_numpy_array
    
    deeptools_matrix
  - Dnaseq_with_reference_genome
    
    Make
    
    S
    
    Sample
  - Ensembl
  - FastQC
  - Fasta
  - Fastq
  - Fastq_sample
    
    Data
    
    Make
    
    Data
  - Fastq_screen
  - Formats
    
    bam
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    fasta
    
    fastq
    
    gff
    
    gff2
    
    gff3
    
    newick
    
    nexus
    
    nhx
    
    phred64_fastq
    
    phylip
    
    sam
    
    sanger_fastq
    
    solexa_fastq
    
    sra
  - Gff
  - Hisat2
  - Htseq
    
    count_tsv
  - Idba
  - Idr
  - Iqtree
  - Jaspar
  - Kallisto
    
    abundance_table
    
    index
  - Macs
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Macs2
    
    broad_peaks
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Meme_suite
  - Ncbi_genome
  - Phyml
  - Picardtools
  - Prokka
  - Quast
  - Raxml
  - SE_or_PE
  - Samtools
  - Spades
  - Sra_toolkit
  - Srst2
  - Star
  - Subread
    
    count_table
  - Tophat
  - Trinity
  - Ucsc_gb
    
    Lift_over
    
    chain_file
    
    bedGraph
    
    bigBed
    
    bigWig
    
    chrom_sizes
    
    twobit
    
    wig
bistro-bio.examples
- Bistro_bio_examples
  - Chen2008
    
    Dnaseq
    
    FQS
    
    Sample
  - Zhou2011

Legend:
Library
Module
Module type
Parameter
Class
Class type

val run_gen_cmd : 
  ?mlst_db:Formats.fasta Bistro.file ->
  ?mlst_delimiter:string ->
  ?mlst_definitions:Formats.fasta Bistro.file ->
  ?mlst_max_mismatch:int ->
  ?gene_db:Formats.fasta Bistro.file list ->
  ?no_gene_details:bool ->
  ?gene_max_mismatch:int ->
  ?min_coverage:int ->
  ?max_divergence:int ->
  ?min_depth:int ->
  ?min_edge_depth:int ->
  ?prob_err:float ->
  ?truncation_score_tolerance:int ->
  ?other:string ->
  ?max_unaligned_overlap:int ->
  ?mapq:int ->
  ?baseq:int ->
  ?samtools_args:string ->
  ?report_new_consensus:bool ->
  ?report_all_consensus:bool ->
  string ->
  Bistro.Shell_dsl.template list ->
  Bistro.Shell_dsl.command

val run_se : 
  ?mlst_db:Formats.fasta Bistro.file ->
  ?mlst_delimiter:string ->
  ?mlst_definitions:Formats.fasta Bistro.file ->
  ?mlst_max_mismatch:int ->
  ?gene_db:Formats.fasta Bistro.file list ->
  ?no_gene_details:bool ->
  ?gene_max_mismatch:int ->
  ?min_coverage:int ->
  ?max_divergence:int ->
  ?min_depth:int ->
  ?min_edge_depth:int ->
  ?prob_err:float ->
  ?truncation_score_tolerance:int ->
  ?other:string ->
  ?max_unaligned_overlap:int ->
  ?mapq:int ->
  ?baseq:int ->
  ?samtools_args:string ->
  ?report_new_consensus:bool ->
  ?report_all_consensus:bool ->
  ?threads:int ->
  Formats.fastq Bistro.file list ->
  [ `srst2 ] Bistro.directory

val run_pe : 
  ?mlst_db:Formats.fasta Bistro.file ->
  ?mlst_delimiter:string ->
  ?mlst_definitions:Formats.fasta Bistro.file ->
  ?mlst_max_mismatch:int ->
  ?gene_db:Formats.fasta Bistro.file list ->
  ?no_gene_details:bool ->
  ?gene_max_mismatch:int ->
  ?min_coverage:int ->
  ?max_divergence:int ->
  ?min_depth:int ->
  ?min_edge_depth:int ->
  ?prob_err:float ->
  ?truncation_score_tolerance:int ->
  ?other:string ->
  ?max_unaligned_overlap:int ->
  ?mapq:int ->
  ?baseq:int ->
  ?samtools_args:string ->
  ?report_new_consensus:bool ->
  ?report_all_consensus:bool ->
  ?threads:int ->
  Formats.fastq Bistro.file list ->
  [ `srst2 ] Bistro.directory