### Verify mrbait Installation (mrbait)

Source: https://mrbait.readthedocs.io/en/latest/installation

This command verifies the successful installation of the mrbait tool and displays its help menu, providing an overview of available options and arguments.

```bash
mrbait -h

```

--------------------------------

### Install MrBait from Source

Source: https://mrbait.readthedocs.io/en/latest/installation

Installs the development version of MrBait by cloning the GitHub repository and using the setup.py script. This method requires manual installation of vsearch and blast if they are not already present. It's suitable for users who need the latest features or want to contribute to development.

```bash
git clone https://github.com/tkchafin/mrbait.git
cd mrbait
python ./setup.py install
```

--------------------------------

### Install MrBait using Conda

Source: https://mrbait.readthedocs.io/en/latest/installation

Installs MrBait and its dependencies using the conda package manager. This is the recommended installation method for most users, as it simplifies dependency management and ensures compatibility. It specifies channels where the mrbait package and its dependencies can be found.

```bash
conda install mrbait -c tylerkchafin -c bioconda -c conda-forge
```

--------------------------------

### Generate and Filter Baits (mrbait)

Source: https://mrbait.readthedocs.io/en/latest/installation

This command generates baits with specified length and tiling parameters, and additionally filters alignments to include only those with 5 or more individuals and a length greater than 500 bases.

```bash
mrbait -M example.maf -b 80 -s tile=40 -l 500 -c 5

```

--------------------------------

### Generate Baits with Specific Parameters (mrbait)

Source: https://mrbait.readthedocs.io/en/latest/installation

This command generates baits of a specified length (e.g., 80) and tiles them across target regions with a defined overlap (e.g., 40 bases) from a Multiple Alignment File (MAF).

```bash
mrbait -M example.maf -b 80 -s tile=40

```

--------------------------------

### Convert FASTA to .loci format using Bash

Source: https://mrbait.readthedocs.io/en/latest/files

This bash script iterates through all FASTA files in the current directory (prefixed with 'example') and converts them into a single '.loci' file. It uses awk to format the FASTA headers and sequences, and appends a '//' delimiter between each alignment block. This is useful for preparing data for MrBait when using reduced-representation sequencing methods.

```bash
for file in `ls example*.fasta`; do
  awk 'BEGIN{ORS=""}$1~/^>/{print $01"\t";next}{print $0"\n"}' $file
  >> example.loci;
  echo "//" >> example.loci;
done

```

--------------------------------

### Run MrBait command for ddRAD dataset

Source: https://mrbait.readthedocs.io/en/latest/benchmarking

This command demonstrates how to run MrBait with a specific ddRAD dataset. It includes parameters for loci file, threads, filtering, and SNP/tile settings. The command is executed on a system with 4 threads, resulting in a total runtime of 392 seconds.

```bash
mrbait -L wtd_run1.loci -T 4 -c 12 -l 150 -b 60 -K 1.0 -d 200 -F snp=1,10 -s tile=30
```

--------------------------------

### FASTA Output with Expanded Ambiguities

Source: https://mrbait.readthedocs.io/en/latest/output

Illustrates the FASTA output when the -x/--expand option is used, showing all possible combinations of ambiguity sequences. This can lead to a significant increase in the number of output sequences.

```fasta
>Locus2_Target4_Bait1.1
ATGTAATAAGGTATATG……
>Locus2_Target4_Bait1.1
ATGTAATGAGGTATATG……
>Locus1_Target4_Bait2.1
TATGAATGTCGCGCGAT……
…
```

--------------------------------

### FASTA Output with Ambiguity Sequences (Default)

Source: https://mrbait.readthedocs.io/en/latest/output

Demonstrates the default FASTA output format for baits, including consensus sequences with ambiguity codes. This format is used when the -x/--expand option is not specified.

```fasta
>Locus1_Target4_Bait1
ATGTAATRAGGTATATG……
>Locus1_Target4_Bait2
TATGAATGTCGCGCGAT……
…
```

--------------------------------

### FASTA Output with Expanded Ambiguities and Reverse Complements

Source: https://mrbait.readthedocs.io/en/latest/output

Shows the FASTA output when both the -x/--expand and --strand both options are used. This includes all expanded ambiguity combinations and their reverse complements, providing a comprehensive set of bait sequences.

```fasta
>Locus2_Target4_Bait1.1
ATGTAATAAGGTATATG……
>Locus2_Target4_Bait1.1_revcomp
TACATTATTCCATATAC……
>Locus2_Target4_Bait1.1
ATGTAATGAGGTATATG……
>Locus2_Target4_Bait1.1_revcomp
TACATTACTCCATATAC ……
>Locus1_Target4_Bait2.1
TATGAATGTCGCGCGAT……
>Locus1_Target4_Bait2.1_revcomp
ATACTTACAGCGCGCTA……
…
```

--------------------------------

### BLAST Filtering Configuration

Source: https://mrbait.readthedocs.io/en/latest/usage

Configure BLAST filtering options within MrBait to refine sequence analysis based on BLAST hits.

```APIDOC
## BLAST Filtering Options

This section details the command-line options available for configuring NCBI-BLAST+ filtering within the MrBait tool.

### Method
N/A (Configuration options for a command-line tool)

### Endpoint
N/A

### Parameters
#### Command-line Flags
- **`--blastn`** (string) - Optional - Path to the blastn binary. Defaults to assuming 'blastn' is in the system's PATH.
- **`--makedb`** (string) - Optional - Path to the makeblastdb binary. Defaults to assuming 'makeblastdb' is in the system's PATH.
- **`--blastdb`** (string) - Required - Full path to a pre-built BLAST-formatted database to search against.
- **`--fastadb`** (string) - Required - Path to a FASTA file if the database needs to be built using `makeblastdb`.
- **`--e_value`** (float) - Optional - Minimum E-value threshold to report BLAST hits. [default=0.000001]
- **`--gapopen`** (integer) - Optional - Penalty for opening gaps during alignment. [default=5]
- **`--gapextend`** (integer) - Optional - Penalty for extending gaps during alignment. [default=2]
- **`--word_size`** (integer) - Optional - Word size for BLAST alignment. [default=11]
- **`--max_hits`** (integer) - Optional - Maximum number of target sequences to report per query. Corresponds to BLAST's `--max_target_seqs`. [default=10000]
- **`--nodust`** (boolean) - Optional - Flag to disable the low-complexity filter in blastn. [default=false]
- **`--megablast`** (boolean) - Optional - Flag to use the megablast algorithm for finding nearly identical alignments. [default=false]

### Usage Examples

**Example 1: Filtering with a pre-built BLAST database**
```bash
mrbait --blastdb /path/to/your/blast_database --e_value 1e-5 --filter_r target_sequences.fasta
```

**Example 2: Filtering with a FASTA database and enabling megablast**
```bash
mrbait --fastadb /path/to/your/fasta_database.fasta --megablast --filter_b bait_sequences.fasta
```

### Response
N/A (This describes command-line arguments, not API responses.)
```

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