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 Genome assembler based on greedy and genetic algorithms written in Go [golang.org]
From second generation sequencing reads to annotated bacterial genome
an attempt to incorporate BLASTp into BUSCO
an investigation into the efficiency of Trinity transcriptome assemblies
Analysis accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" http://genome.cshlp.org/content/early/2017/03/20/gr.216465.116.full.pdf
Android application for detection & removal of false overlaps occurred during the genome assembly process
Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97
An efficient approach for constructing de-bruijn graph for genome assembly
Fast and memory-efficient noisy read overlapping with KD-trees
Hierarchical scaffold/assembly graph web visualization tool. As of August 9, 2017, the official repository for this has moved to MarBL! Use that repository instead :)
A pipeline for viral identification from metagenomic samples
example genomics workflow for student training
This pipeline will check assembly and annotations based on gene families.
find large indels (in the blind spot between GATK/freebayes and SV callers)
Python script for comparing two genome assemblies
Assembled Phi-X174 genome using Overlap Graph, Kmer Composition and De-Bruijn Graph.
Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.
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