Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

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.

BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper

Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.

Generate interactive dotplot from mummer4 output using plotly

Pipelines for the production of Treeval data

Fast and simple algorithms for computing both LCSk and LCSk+

Phasing reads with secondary alignments

easy_circos is a simple conda package that aims on rapidly and easily creating minimal circos configurations templates based on input data.

A package for handling whole genome alignments by Pádraic Corcoran and Henry Barton

Parsimonious delimitation of large SNP datasets using the four gamete test

A utility to call polyA sites based on genome alignments in SAM format

ReadXplorer - Visualization and Analysis of Mapped Sequences

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

Scripts to index and align Bovine genome with HISAT2

A comparative annotation toolkit (CAT) pipeline for 304 fly genomes.

Maximum Acyclic Subgraph (MAS) - Multiple Sequence Alignment (MSA) Game

command-line interface software for genome alignment