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
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Updated
Dec 17, 2013
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
A utility to call polyA sites based on genome alignments in SAM format
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
Docker to run BWA for aligning sequences against a reference genome
Scripts to index and align Bovine genome with HISAT2
Fast and simple algorithms for computing both LCSk and LCSk+
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.
Maximum Acyclic Subgraph (MAS) - Multiple Sequence Alignment (MSA) Game
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.
Multiple python implementations that compute the global, local, and end-gap free alignments of genomes.
Parsimonious delimitation of large SNP datasets using the four gamete test
A package for handling whole genome alignments by Pádraic Corcoran and Henry Barton
Generate interactive dotplot from mummer4 output using plotly
a genome alignment library built around seed-and-extend algorithms for maximal exact and unique matches
command-line interface software for genome alignment
BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
ReadXplorer - Visualization and Analysis of Mapped Sequences
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