Tool Reference

This page provides comprehensive documentation for all bioinformatics tools supported by the configuration system.

Overview

Each tool configuration follows consistent patterns: - threads: Number of CPU threads to allocate
- options: CLI options string with validation and filtering - sub-configurations: Some tools have multiple operational modes

Tool Categories

Alignment Tools

• bowtie2 - Bowtie2 aligner configuration
• star - STAR RNA-seq aligner configuration

Processing Tools

• samtools - Samtools suite configuration
• picard - Picard tools configuration

Trimming Tools

• cutadapt - Cutadapt trimming configuration

Peak Calling Tools

• macs - MACS peak caller configuration
• lanceotron - Lanceotron peak caller configuration
• seacr - SEACR peak caller configuration

Analysis Tools

• deeptools - Deeptools suite configuration
• homer - HOMER suite configuration
• bamnado - Bamnado coverage analysis configuration
• subread - Subread feature counting configuration

Specialized Tools

• methyldackel - Methyldackel methylation analysis configuration
• bcftools - BCFtools variant calling suite configuration

Other Tools

• fastq_screen - FastqScreen configuration
• fastqc - FastQC quality control configuration
• lanceotron_mcc - Lanceotron MCC configuration
• mageck - MAGeCK CRISPR screen analysis configuration
• meme - MEME Suite motif analysis configuration
• qualimap - Qualimap quality control configuration
• salmon - Salmon quantification configuration
• trim_galore - Trim Galore configuration

---

Detailed Tool Documentation

---

fastq_screen

FastqScreen configuration

FastqScreen tool configuration.

Configuration Structure

Inherits from: ToolConfig

Fields

threads

Number of threads to use

Type: <class 'int'>

Default: 1

command_line_arguments

CLI options

Type: <class 'seqnado.config.third_party_tools.CommandLineArguments'>

Default: PydanticUndefined

Sub-configuration: See command_line_arguments details

config

Path to FastqScreen configuration file

Type: <class 'str'>

Default: ``

Sub-configurations

Command_Line_Arguments Configuration

Base class for CLI options with validation and filtering capabilities.

Fields

value: CLI options string (default: ``)

exclude: Options to exclude from the final command

include: Options to include in the final command

---

fastqc

FastQC quality control configuration

FastQC quality control tool configuration.

Configuration Structure

Inherits from: ToolConfig

Fields

threads

Number of threads to use

Type: <class 'int'>

Default: 1

command_line_arguments

CLI options

Type: <class 'seqnado.config.third_party_tools.CommandLineArguments'>

Default: PydanticUndefined

Sub-configuration: See command_line_arguments details

Sub-configurations

Command_Line_Arguments Configuration

Base class for CLI options with validation and filtering capabilities.

Fields

value: CLI options string (default: ``)

exclude: Options to exclude from the final command

include: Options to include in the final command

---

qualimap

Qualimap quality control configuration

Qualimap quality control tool configuration.

Configuration Structure

Inherits from: ToolConfig

Fields

threads

Number of threads to use

Type: <class 'int'>

Default: 1

command_line_arguments

CLI options

Type: <class 'seqnado.config.third_party_tools.CommandLineArguments'>

Default: PydanticUndefined

Sub-configuration: See command_line_arguments details

Sub-configurations

Command_Line_Arguments Configuration

Base class for CLI options with validation and filtering capabilities.

Fields

value: CLI options string (default: ``)

exclude: Options to exclude from the final command

include: Options to include in the final command

---

bowtie2

Bowtie2 aligner configuration

Bowtie2 alignment tool configuration.

Configuration Structure

Fields

align

Alignment configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See align details

index

Index building configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See index details

Sub-configurations

Align Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Index Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

star

STAR RNA-seq aligner configuration

STAR RNA-seq aligner configuration.

Configuration Structure

Fields

align

Alignment configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See align details

index

Index building configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See index details

Sub-configurations

Align Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Index Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

samtools

Samtools suite configuration

Samtools suite configuration.

Configuration Structure

Fields

sort

Sort configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See sort details

index

Index configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See index details

view

View configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See view details

merge

Merge configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See merge details

Sub-configurations

Sort Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Index Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

View Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Merge Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

picard

Picard tools configuration

Picard tools configuration.

Configuration Structure

Fields

mark_duplicates

Mark duplicates configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See mark_duplicates details

Sub-configurations

Mark_Duplicates Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

cutadapt

Cutadapt trimming configuration

Cutadapt adapter trimming tool configuration.

When mode='crispr', adapters are auto-detected from FASTQ files. Otherwise, specify adapters in command_line_arguments.

Configuration Structure

Inherits from: ToolConfig

Fields

threads

Number of threads to use

Type: <class 'int'>

Default: 1

command_line_arguments

CLI options

Type: <class 'seqnado.config.third_party_tools.CommandLineArguments'>

Default: PydanticUndefined

Sub-configuration: See command_line_arguments details

mode

Cutadapt mode: 'crispr' for auto-detection, 'default' for manual

Type: <enum 'CutadaptMode'>

Default: CutadaptMode.CRISPR

Possible values: default, crispr

Enums

cutadapt {#cutadapt}Mode

Create a collection of name/value pairs.

Example enumeration:

class Color(Enum): ... RED = 1 ... BLUE = 2 ... GREEN = 3

Access them by:

• attribute access:

Color.RED

• value lookup:

Color(1)

• name lookup:

Color['RED']

Enumerations can be iterated over, and know how many members they have:

len(Color) 3

list(Color) [, , ]

Methods can be added to enumerations, and members can have their own attributes -- see the documentation for details.

Name	Value
DEFAULT	default
CRISPR	crispr

Sub-configurations

Command_Line_Arguments Configuration

Base class for CLI options with validation and filtering capabilities.

Fields

value: CLI options string (default: ``)

exclude: Options to exclude from the final command

include: Options to include in the final command

---

trim_galore

Trim Galore configuration

Trim Galore adapter trimming tool configuration.

Configuration Structure

Fields

trim

Trimming configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See trim details

Sub-configurations

Trim Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

macs

MACS peak caller configuration

MACS peak calling tool configuration with mode-specific defaults.

Configuration Structure

Fields

version

MACS version to use

Type: typing.Literal['2', '3']

Default: 3

mode

Analysis mode

Type: <enum 'MacsMode'>

Default: MacsMode.GENERIC

Possible values: atac, chip_broad, chip_tf, generic

call_peaks

Peak calling configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Sub-configuration: See call_peaks details

Enums

macs {#macs}Mode

Create a collection of name/value pairs.

Example enumeration:

class Color(Enum): ... RED = 1 ... BLUE = 2 ... GREEN = 3

Access them by:

• attribute access:

Color.RED

• value lookup:

Color(1)

• name lookup:

Color['RED']

Enumerations can be iterated over, and know how many members they have:

len(Color) 3

list(Color) [, , ]

Methods can be added to enumerations, and members can have their own attributes -- see the documentation for details.

Name	Value
ATAC	atac
CHIP_BROAD	chip_broad
CHIP_TF	chip_tf
GENERIC	generic

Sub-configurations

Call_Peaks Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

lanceotron

Lanceotron peak caller configuration

Lanceotron peak calling tool configuration.

Configuration Structure

Fields

call_peaks

Peak calling configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See call_peaks details

Sub-configurations

Call_Peaks Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

lanceotron_mcc

Lanceotron MCC configuration

Lanceotron MCC peak calling tool configuration.

Configuration Structure

Inherits from: ToolConfig

Fields

threads

Number of threads to use

Type: <class 'int'>

Default: 1

command_line_arguments

CLI options

Type: <class 'seqnado.config.third_party_tools.CommandLineArguments'>

Default: PydanticUndefined

Sub-configuration: See command_line_arguments details

Sub-configurations

Command_Line_Arguments Configuration

Base class for CLI options with validation and filtering capabilities.

Fields

value: CLI options string (default: ``)

exclude: Options to exclude from the final command

include: Options to include in the final command

---

seacr

SEACR peak caller configuration

SEACR peak calling tool configuration (non-ToolConfig based).

Configuration Structure

Fields

threshold

Peak calling threshold

Type: <class 'float'>

Default: 0.01

normalization

Normalization method

Type: <class 'str'>

Default: non

stringency

Peak calling stringency

Type: typing.Literal['stringent', 'relaxed']

Default: stringent

---

deeptools

Deeptools suite configuration

Deeptools suite configuration.

Configuration Structure

Fields

bam_coverage

BAM coverage configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See bam_coverage details

compute_matrix

Compute matrix configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See compute_matrix details

plot_heatmap

Plot heatmap configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See plot_heatmap details

Sub-configurations

Bam_Coverage Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Compute_Matrix Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Plot_Heatmap Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

homer

HOMER suite configuration

HOMER motif analysis suite configuration.

Configuration Structure

Fields

make_tag_directory

Tag directory creation configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See make_tag_directory details

make_bigwig

BigWig creation configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See make_bigwig details

annotate_peaks

Peak annotation configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See annotate_peaks details

find_peaks

Peak finding configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See find_peaks details

find_motifs_genome

Motif finding configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See find_motifs_genome details

known_motif_db

Path to known motif database file

Type: <class 'str'>

Sub-configurations

Make_Tag_Directory Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Make_Bigwig Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Annotate_Peaks Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Find_Peaks Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Find_Motifs_Genome Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

meme

MEME Suite motif analysis configuration

MEME Suite motif analysis configuration.

Configuration Structure

Fields

meme_chip

MEME-ChIP motif analysis configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See meme_chip details

known_motif_db

Path to known motif database file

Type: <class 'str'>

Sub-configurations

meme {#meme}_Chip Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

bamnado

Bamnado coverage analysis configuration

Bamnado coverage analysis tool configuration.

Configuration Structure

Fields

bam_coverage

BAM coverage analysis configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See bam_coverage details

bigwig_compare

BigWig comparison configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See bigwig_compare details

bigwig_aggregate

BigWig aggregation configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See bigwig_aggregate details

Sub-configurations

Bam_Coverage Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Bigwig_Compare Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Bigwig_Aggregate Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

subread

Subread feature counting configuration

Subread feature counting tool configuration.

Configuration Structure

Fields

feature_counts

Feature counting configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See feature_counts details

Sub-configurations

Feature_Counts Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

salmon

Salmon quantification configuration

Salmon quantification tool configuration.

Configuration Structure

Fields

quant

Quantification configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See quant details

Sub-configurations

Quant Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

methyldackel

Methyldackel methylation analysis configuration

Methyldackel methylation analysis tool configuration.

Configuration Structure

Inherits from: ToolConfig

Fields

threads

Number of threads to use

Type: <class 'int'>

Default: 1

command_line_arguments

CLI options

Type: <class 'seqnado.config.third_party_tools.CommandLineArguments'>

Default: PydanticUndefined

Sub-configuration: See command_line_arguments details

Sub-configurations

Command_Line_Arguments Configuration

Base class for CLI options with validation and filtering capabilities.

Fields

value: CLI options string (default: ``)

exclude: Options to exclude from the final command

include: Options to include in the final command

---

bcftools

BCFtools variant calling suite configuration

BCFtools variant calling suite configuration.

Configuration Structure

Fields

call

Variant calling configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See call details

consensus

Consensus calling configuration

Type: <class 'seqnado.config.third_party_tools.ToolConfig'>

Default: PydanticUndefined

Sub-configuration: See consensus details

Sub-configurations

Call Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

Consensus Configuration

Base configuration for a tool with threads and CLI options.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

---

mageck

MAGeCK CRISPR screen analysis configuration

MAGeCK CRISPR screen analysis tool configuration.

Configuration Structure

Fields

count

MAGeCK count configuration for guide RNA quantification

Type: <class 'seqnado.config.third_party_tools.MageckCount'>

Default: PydanticUndefined

Sub-configuration: See count details

test

MAGeCK test (RRA) configuration for comparing treatment vs control

Type: <class 'seqnado.config.third_party_tools.MageckTest'>

Sub-configuration: See test details

mle

MAGeCK MLE configuration for complex experimental designs

Type: <class 'seqnado.config.third_party_tools.MageckMLE'>

Default: PydanticUndefined

Sub-configuration: See mle details

sgrna_library

Path to sgRNA library file (.txt or .csv format)

Type: <class 'str'>

design_matrix

Path to design matrix file for MAGeCK MLE analysis

Type: <class 'str'>

control_sgrna

Comma-separated list of control sgRNA IDs or file path (prefix with --control-sgrna)

Type: <class 'str'>

control_gene

Comma-separated list of control gene names or file path (prefix with --control-gene)

Type: <class 'str'>

Sub-configurations

Count Configuration

MAGeCK count configuration.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

norm_method: Normalization method for read counts (default: median)

pdf_report: Generate PDF quality control report (default: False)

Test Configuration

MAGeCK test (RRA) configuration.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)

control_samples: Comma-separated list of control sample labels

treatment_samples: Comma-separated list of treatment sample labels

Mle Configuration

MAGeCK MLE configuration.

Fields

threads: Number of threads to use (default: 1)

command_line_arguments: CLI options (default: PydanticUndefined)