malonge

malonge's Stars

• mamba-org/mamba

  The Fast Cross-Platform Package Manager

  Language:C++7k461.8k368

• bioconda/bioconda-recipes

  Conda recipes for the bioconda channel.

  Language:Shell1.7k961.9k3.3k

• samtools/samtools

  Tools (written in C using htslib) for manipulating next-generation sequencing data

  Language:C1.6k1001.3k580

• martinus/robin-hood-hashing

  Fast & memory efficient hashtable based on robin hood hashing for C++11/14/17/20

  Language:C++1.5k41130147

• marbl/CHM13

  The complete sequence of a human genome

  928689499

• marbl/canu

  A single molecule sequence assembler for genomes large and small.

  Language:C++664542.3k179

• igvteam/igv.js

  Embeddable genomic visualization component based on the Integrative Genomics Viewer

  Language:HTML650341.2k230

• agshumate/Liftoff

  An accurate GFF3/GTF lift over pipeline

  Language:Python448715554

• gpertea/gffread

  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

  Language:C++382913539

• maickrau/GraphAligner

  Language:C++2631510133

• alekseyzimin/masurca

  Language:M42481634635

• dfguan/purge_dups

  haplotypic duplication identification tool

  Language:C217914923

• Nextomics/NextPolish

  Fast and accurately polish the genome generated by long reads.

  215614028

• nanoporetech/megalodon

  Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

  Language:Python1982134730

• marbl/SALSA

  SALSA: A tool to scaffold long read assemblies with Hi-C data

  Language:Python1822016547

• lh3/kmer-cnt

  Code examples of fast and simple k-mer counters for tutorial purposes

  Language:C++16710915

• ekg/seqwish

  alignment to variation graph inducer

  Language:C++143146618

• arangrhie/T2T-Polish

  Evaluation and polishing workflows for T2T genome assemblies

  Language:Shell112988

• lh3/hickit

  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

  Language:C10883511

• mahulchak/svmu

  A program to call variants from genome alignment

  Language:C++7652718

• univieCUBE/gepard

  Genome Pair Rapid Dotter

  Language:Java6251216

• ablab/TandemTools

  Tool for assessing/improving assembly quality in extra-long tandem repeats

  Language:C++468105

• lh3/calN50

  Compute N50/NG50 and auN/auNG

  Language:JavaScript31412

• sanger-tol/PretextView

  OpenGL Powered Pretext Contact Map Viewer

  Language:C305258

• LeanQ/SPLITREADER

  Split-read pipeline for the identification of non-reference TE insertions with TSDs

  Language:Shell24129

• esolares/HapSolo

  Reduction of Althaps and Duplicate Contigs for Improved Hi-C Scaffolding

  Language:Python193106

• medvedevgroup/BubbZ

  Language:C++15511

• mkirsche/Grafter

  Scaffolding with Ultralong Reads

  Language:Java14301

• mkirsche/vcfigv

  Code for generating IGV screenshots from VCF files

  Language:Java7200

• mschatz/genometools

  Collection of smaller utilities and helper scripts

  Language:C++3201