G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.
BiSulfite Bolt - A Bisulfite Sequencing Alignment and Processing Tool
DNAssist: the integrated editing and analysis of molecular biology sequences in Windows
A pure python lazy BAM parser
web application for DNA comparison, alignment and phylogenetic tree. Released on 2020.
A fast, accurate and configurable seeding framework for short-read DNA sequence alignment
DNA barcoding analysis pipeline
Parallel-DNA-Sequence-Alignment
This is a bunch of programs I created in the 2020 Intermediate Coding For Medicine Course. No Stealing.
Import and export .SAM (Sequence Alignment/Map format) files in Mathematica
Rank and filter BLAST DNA sequence matches using probabilities and a heuristic scoring model.
Guide to download NCBI Bioproject sequencing data and script to generate DNA short read alignment dataset from the data.
A couple of assignments I did for a course in computational (molecular) biology @ University of Warsaw
Command-line tool for global protein/DNA sequence alignment using a simplified version of the Needleman-Wunsch algorithm
The project is based on the paper Sequence Alignment by Cross-Correlation and bridges the gap between the knowledge and an useful implementation.
Bowtie2 v2.5.2 Dockerfile Native for Apple M1+ Silicon (ARM64) and Intel/AMD (x86_64) Containers
This is a repo for the algorithms solutions towards the DNA alignment problem. I adopt two ways to solve the problem: dp and Divide n' Conquer
An automated cloud-based pipeline for Sanger sequencing QC, read merging, primer trimming, and NCBI BLAST identification via Google Colab.
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