abi processing

Processing Sanger Sequencing file (abi) wiht Python or R

In R, you can using sangerseqR to reading ab1 file.
An example can see: Karobben 2020

Python

Biopython

from Bio import SeqIO
handle = open("test.ab1", "rb")
for record in SeqIO.parse(handle, "abi"):
    print(record)

Trace plot

Biopython: Click hear

Package sanger-sequencing

Link
Can’t find any examples…

Perl

ABIF

Convert abi to Scf

reference: stock overflow

convert_trace -out_format scf < trace.ab1 > trace.scf

Convert ab1 to excel

Working Manual: ab1_organizer

pip install ab1_organizer

ab1_organizer.py -f ./path/to/zip/file -t ./path/to/order/table.xlsx

Base Calling

GitHub: tracy
Documentation
Paper

(PS: It seems like we need to download some files from google. So, as you can see, it’s not easy for the people in China mainland to install it.)
It is a great app for basecalling, alignment, assembly and deconvolution of sequencing chromatogram files.

Installation

apt install \
    build-essential g++ \
    cmake \
    git-all \
    liblzma-dev \
    zlib1g-dev \
    libbz2-dev \
    liblzma-dev \
    libboost-date-time-dev \
    libboost-program-options-dev \
    libboost-system-dev \
    libboost-filesystem-dev \
    libboost-iostreams-dev

git clone --recursive https://github.com/gear-genomics/tracy.git
cd tracy/
make all
make install
./bin/tracy -h