malonge

malonge's Stars

• jmschrei/pomegranate

  Fast, flexible and easy to use probabilistic modelling in Python.

  Language:Python3.4k95788589

• thomasp85/patchwork

  The Composer of ggplots

  Language:R2.5k46362162

• pydata/numexpr

  Fast numerical array expression evaluator for Python, NumPy, Pandas, PyTables and more

  Language:Python2.3k61382214

• bwa-mem2/bwa-mem2

  The next version of bwa-mem

  Language:C++72935215102

• fritzsedlazeck/Sniffles

  Structural variation caller using third generation sequencing

  Language:Python5732749895

• jmschrei/apricot

  apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly. See the documentation page: https://apricot-select.readthedocs.io/en/latest/index.html

  Language:Jupyter Notebook49993348

• DaehwanKimLab/hisat2

  Graph-based alignment (Hierarchical Graph FM index)

  Language:C++48738361121

• lh3/minigraph

  Sequence-to-graph mapper and graph generator

  Language:C4272811838

• marbl/merqury

  k-mer based assembly evaluation

  Language:Shell2971114721

• chanzuckerberg/shasta

  [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

  Language:C++2722310658

• marbl/Winnowmap

  Long read / genome alignment software

  Language:C268164723

• deeptools/HiCExplorer

  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

  Language:Python2371563470

• abyzovlab/CNVnator

  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

  Language:C++2122027166

• lbcb-sci/racon

  Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

  Language:C++207126034

• mkirsche/Jasmine

  Jasmine: SV Merging Across Samples

  Language:Java189115818

• VGP/vgp-assembly

  VGP repository for the genome assembly working group

  Language:Shell188262351

• lh3/cgranges

  A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

  Language:C165121018

• linsalrob/fastq-pair

  Match up paired end fastq files quickly and efficiently.

  Language:C14452232

• deehzee/unionfind

  A union-find disjoint sets data structure implemented in Python with the "Weighted Quick Union with Path Compression" algorithm.

  Language:Python665321

• SAMtoBAM/MUMandCo

  MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation

  Language:Shell6523115

• human-pangenomics/hpgp-data

  Data from the Human PanGenomics Project

  6010124

• schatzlab/crossstitch

  Code for phasing SVs with SNPs

  Language:Java528153

• HajkD/LTRpred

  De novo annotation of young retrotransposons

  Language:R465278

• mkirsche/Iris

  A module for improving the insertion sequences of structural variant calls

  Language:Java29295

• yangao07/TideHunter

  TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

  Language:C275124

• volkansevim/alpha-CENTAURI

  A python package from Pacific Biosciences to analyze centromeric sequences

  Language:Python21934

• MariaNattestad/Nchart

  Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file

  Language:R10205

• srividya22/geneLift

  Gene model transfer from closely related reference genomes using cDNA alignments

  Language:Python10242

• robbylewis7/Tastify

  Language:JavaScript1100

• zlemmon/physalis-yellow-mapping

  code for mapping the yellow flower mutant in Physalis pruinosa

  Language:HTML1101