Beginner’s Guide to Useful Bash Commands for Handling FASTA Files

Understanding FASTA Files

FASTA files are standard text-based files in bioinformatics used to represent nucleotide or protein sequences. They include:

1. A header line starting with > followed by an identifier and optional description.
2. One or more lines of sequence data (nucleotides or amino acids).

Why Bash Commands for FASTA?

Using Bash:

• Simplifies repetitive tasks.
• Allows rapid and efficient data manipulation without large software packages.
• Is highly customizable and versatile.

Bash Commands for Basic FASTA Manipulations

1. Count the Number of Sequences

Count sequences (headers start with >):

2. Extract Headers Only

3. Count Total Characters in a Sequence

4. Linearize FASTA (Remove Wrapping)

5. Extract Specific Sequence by ID

Intermediate Bash Commands

6. Find Sequences Starting with Specific Base

To list headers where sequences start with A:

7. Add Prefix or Suffix to Headers

Add a prefix:

Add a suffix:

8. Remove Duplicate Sequences

Advanced Bash Commands

9. Compute GC Content for Each Sequence

10. Reverse Complement a Sequence

11. Extract Sequences Longer Than X

Recent Tools and Trends

12. Use seqkit for Enhanced Functionality

seqkit is a recent and powerful toolkit for FASTA/FASTQ processing. Example commands:

• Count sequences:
  bash

  Copy code

  seqkit stats file.fasta

• Extract subsequences:
  bash

  Copy code

  seqkit subseq --chr start:end file.fasta

• Filter by length:
  bash

  Copy code

  seqkit seq -m 100 file.fasta > filtered.fasta


13. Parallel Processing with GNU Parallel

Speed up large FASTA file operations:

14. Randomize or Shuffle Sequences

Randomize sequence order using shuf:

Applications

1. Genome Analysis: Filter out low-quality sequences or subsequences.
2. Protein Analysis: Compute metrics like molecular weight or GC content.
3. Pipeline Integration: Use Bash commands in bioinformatics pipelines for preprocessing data.

Why Learn These Commands?

• Empowerment to handle complex data directly in the terminal.
• Efficiently process large-scale sequence datasets.
• Leverage cutting-edge tools and techniques for modern research.

This guide ensures beginners can confidently handle and manipulate FASTA files using Bash, while also introducing advanced tools and trends for seasoned bioinformaticians.