SangSeqFuse

SangSeqFuse is a lightweight Bash script that converts forward and reverse Sanger sequencing trace files (.ab1) into a consensus FASTA sequence. It performs sequence extraction, reverse complementing, pair-wise alignment, and consensus generation, all in one command-line tool. Popular tools like CAP3 or Phred/Phrap/Consed for creating consensus sequences can often be overly strict or complex for basic Sanger read merging, especially when dealing with short, noisy reads or small-scale sequencing. This tool fixes that problem, especially if the goal to simply create a consensus sequence for performing nBLAST or for building phylogenetic trees.

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Features

• Accepts .ab1 Sanger sequencing trace files (forward and reverse)
• Converts to FASTA using Biopython
• Reverse-complements the reverse strand using EMBOSS seqret
• Aligns reads using MAFFT
• Generates a consensus sequence using EMBOSS cons
• Saves intermediate files and final output in organized directories

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Requirements

Make sure the following tools are installed and accessible in your $PATH:

Tool	Description
mafft	Multiple sequence alignment
cons	EMBOSS tool to generate consensus
seqret	EMBOSS tool for sequence transformation
biopython	for parsing

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Installation

Clone the repository and make the script executable:

git clone https://github.com/demboc/sangseqfuse
cd sangseqfuse
chmod +x sangseqfuse.sh

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Usage

Make sure to have your sequences located in the same directory as sangseqfuse.sh or you can have sangseqfuse.sh installed in your $PATH

./sangseqfuse.sh --forward F.ab1 --reverse R.ab1 --prefix Sample1 --output myconsensus.fasta

Parameters

Flag	Description
-f, --forward	Path to the forward .ab1 file
-r, --reverse	Path to the reverse .ab1 file
-p, --prefix	Prefix for intermediate/final file labeling (this will also be your fasta header)
-o, --output	Name of the output consensus FASTA file
-h, --help	Show usage information