miscellaneous stand-alone basic utilities for genomics and genomics-adjacent operations (share with lab mates)

Pipeline para montagem direcionada (gene-a-gene) a partir de leituras pareadas.

Variant calling pipeline (Snakemake workflow)

This repository covers research paper implementations in the field of Genomics, Next Generation Sequencing, Bioinformatics and Machine Learning.

Detection of unknown genetically modified organisms

AminoExtract is a tool for translating and extracting amino acid sequences from nucleotide-sequences based on a GFF input

This project plots the effect of selecting different kmer length parameter in 2 different de novo genome assembly tools - AbySS and Velvet.

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

A repository to benchmark and automate genome assembly evaluation. Utilize scripts for Dragonflye with diverse polishing models on Illumina and Nanopore reads to fine-tune genome assemblies

Coverage graph creator from BAM files (included in the SSV-Conta package)

SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.

Metrics App is a bioinformatics application developed in Python and Streamlit for calculate Depth of Coverage and Breadth of Coverage from BAM/CRAM files.

Professional MCP server for FastQC and MultiQC quality control analysis with advanced visualization and report parsing

Protein Analysis and Classifier Toolkit

Bioinformatics is a field of information technology and biological science, which use to managing, storing and analyzing these biological data such as DNA, RNA and protein, In this repository I'm use python to create various types of program for analyzing biological data

Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).

Python scripts for design of 5'/3' RACE-based NGS panels, and the following data analysis

Files pertaining to the processing of NGS data in .fasta.gz format for the purposes of identifying the genomic sequences which belong to either of the tuataras dual mitochondrial genomes.

CRISPRSeqSim is a tool that simulates results of CRISPR/cas editing fragments target sequencing.