BacSeq is an all-in-one pipeline for bacterial genome analysis. The software contained several Bioinformatics tools for quality control of raw reads, genome assembly and quality assessments, genome annotation, downstream analysis, and comparative genomic analysis. BacSeq is available for both short-read and long-read sequencing data and the visualization and reports will be exhibited on the HTML page.
- Quality Control
- FastQC
- MultiQC
- Trimming
- fastp
- Assembly
- SPAdes
- Unicycler
- Quality assessment
- QUAST
- Completeness assessment
- BUSCO
- Annotation
- Prokka
- Functional annotation
- eggNOG-mapper
- Downstream analysis
- ABRicate
- StarAMR
- Run-dbcan
- CRISPRCasFinder
- Comparative analysis
- Roary
- SNP-site
- FastTree
- Visualization and report
- ete3
- Conda
bash Miniconda3-latest-Linux-x86_64.sh
git clone https://github.com/mecobpsu/bacseq.git
cd bacseq
source install.sh
# Run the program with a code below
source run_BacSeq.sh
1.Home Page then select Browse... and select Basic mode or Advanced mode
- Quick mode will be running all steps in the pipeline.
- Advanced mode will be running the programs according to your selection.
2.Select directory that include with this files pattern
3.De novo assembly page
4.Downstream analysis page
5.Comparative analysis page
6.Visualization and report page
- Button will be enabled to click when each program runs successfully.
- When the user clicks the button on this page, the program will open an output directory.
- Komwit Surachat
- E-mail: komwit.s@psu.ac.th
- Arnon Chukamnerd
- E-mail: arnonchukamnerd@hotmail.com
- Kongpop Jeenkeawpiam
- E-mail: kongpop.je@gmail.com