SequenceForge-Lite

SequenceForge-Lite is a lightweight tool designed to work with biological sequence data, providing various functionalities for filtering FASTQ files and manipulating FASTA files. Additionally, it offers utilities for parsing BLAST output files.

Code & full README
Usage Guide

Features

FASTQ Filtering

• Filter FASTQ files based on GC content, sequence length, and quality score.
• Specify custom ranges for GC content and sequence length.
• Set a minimum quality score threshold for sequences.

FASTA File Manipulation

• Get quick info on each sequence in FASTA file.
• Convert multiline FASTA files to one-line format.
• Shift the start position of one-line FASTA sequences by a specified amount.

BLAST Output Parsing

• Extract the top hit for each query from BLAST output files.
• Results are sorted alphabetically for easy analysis.

DNA, RNA & amino acid classes

• Calculates GC content in DNA and RNA sequences.
• Prints complement sequence for DNA.
• Transcribes DNA sequence to RNA.
• Prints RNA sequence in codons.
• Finds motifs in nucleic acids sequences.
• Translates RNA sequence to amino acid (without biological meaning, it does it “dumbly”).
• Calculates molecular weight of amino acid sequence.

Custom RandomForestClassifier

• Self written implementation of RandomForestClassifier.
• Has parallelisation functionality (speeds up 2 times when specifying 2 threads).