Calculate Peak-to-Trough Ratio (PTR), plot coverage graph, and perform quality control over contigs in a single pipeline integrating Glimmer3, Bowtie2, Sickle, and algorithms in R.
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Updated
Aug 15, 2019 - C
Calculate Peak-to-Trough Ratio (PTR), plot coverage graph, and perform quality control over contigs in a single pipeline integrating Glimmer3, Bowtie2, Sickle, and algorithms in R.
Final project for Big Data, Small Languages, Scalable Systems course at JHU: Performs alignment between reads and a reference genome sequence using fast fourier transform
Docker to run BWA for aligning sequences against a reference genome
intergenic region analyzer from protein alignments to draft genomes.
stitching coding regions from exon alignments for the protein to genome alignments.
preparing and visualizing proteome to genome alignments
A comparative annotation toolkit (CAT) pipeline for 304 fly genomes.
protein-annotator python package for analyzing protein alignments to draft genomes.
from protein alignments to deep learning preparatory.
alignment visualization and phylogeny plotting for genome aliged regions.
Parsimonious delimitation of large SNP datasets using the four gamete test
Maximum Acyclic Subgraph (MAS) - Multiple Sequence Alignment (MSA) Game
a genome alignment library built around seed-and-extend algorithms for maximal exact and unique matches
command-line interface software for genome alignment
ReadXplorer - Visualization and Analysis of Mapped Sequences
Multiple python implementations that compute the global, local, and end-gap free alignments of genomes.
Workshops, Course Schedule and Teaching Assistant Review from my time as a chosen Undergraduate Teaching Assistant for the University of Pittsburgh course, BIOSC1540 - Computational Genomics taught by Dr. Miler Lee.
Scripts to index and align Bovine genome with HISAT2
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