tahashmi

tahashmi's Stars

• hail-is/hail

  Cloud-native genomic dataframes and batch computing

  Language:Python985552.4k247

• pangenome/pggb

  the pangenome graph builder

  Language:Shell4041417844

• schneebergerlab/plotsr

  Tool to plot synteny and structural rearrangements between genomes

  Language:Python29158628

• PapenfussLab/gridss

  GRIDSS: the Genomic Rearrangement IDentification Software Suite

  Language:Java2602265971

• lbcb-sci/racon

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

  Language:C++206126034

• hartwigmedical/hmftools

  Various algorithms for analysing genomics data

  Language:Java1991947360

• LooseLab/readfish

  CLI tool for flexible and fast adaptive sampling on ONT sequencers

  Language:Python1701427534

• ablab/IsoQuant

  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

  Language:Python1541320714

• nygenome/lancet

  Microassembly based somatic variant caller for NGS data

  Language:C154145833

• hatchet/hatchet

  Analyze graph/hierarchical performance data using pandas dataframes

  Language:Python109911437

• KolmogorovLab/Severus

  A tool for somatic structural variant calling using long reads

  Language:Python1065325

• xjtu-omics/SVision

  Detecting genome structural variants with deep learning in single molecule sequencing

  Language:Python10263810

• friend1ws/nanomonsv

  SV detection tool for nanopore sequence reads

  Language:Python8986212

• antmicro/google-coral-baseboard

  Antmicro's open hardware baseboard for the Google Coral i.MX8 + Edge TPU SoM

  69151230

• raphael-group/hatchet

  HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

  Language:Roff691413832

• katerinakazantseva/strainy

  Graph-based assembly phasing

  Language:Python685305

• antmicro/zynq-video-board

  Open Hardware carrier board supporting modules with Zynq 7000 All Programmable SoC devices.

  5313030

• ICGC-TCGA-PanCancer/TumorType-WGS

  Classifying tumor types based on Whole Genome Sequencing (WGS) data

  Language:R4610522

• djnavarro/arrow-user2022

  Larger-Than-Memory Data Workflows with Apache Arrow

  Language:HTML452244

• TheJacksonLaboratory/Picky

  Structural Variants Pipeline for Long Reads

  Language:Perl4410146

• fulcrumgenomics/python-snakemake-template

  A template repository for Snakemake pipepline(s) and a python command-line toolkit.

  Language:Python271150

• TheJacksonLaboratory/ChIA-PIPE

  ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization

  Language:C279312

• snurk/sg_sandbox

  Experimental String Graph construction and processing

  Language:Python25421

• asherliu/simd-x

  SIMD-X: Programming and Processing of Graph Algorithms on GPUs [USENIX ATC '19]

  Language:Objective-C18306

• aganezov/RCK

  RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes

  Language:Python17414

• Magdoll/MagPhase

  Phasing for metagenomics using PacBio long reads

  Language:Python17433

• polyactis/Accucopy

  Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.

  Language:C++152234

• raphael-group/hatchet-paper

  Related to (Zaccaria and Raphael, 2018), the repository contains the simulated data, the results of all methods involved in the comparison, the results of HATCHet on the prostate and pancreas cancer datasets, and all data and analysis related to these last two cancer datasets.

  Language:Python101101

• PMBio/mb-nanopore-2022

  Analysis code for publication "Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signature"

  Language:Python6141

• usnistgov/giab-pFDA-2nd-challenge

  Code and intermediate data used to generate figures and results for the manuscript describing the challenge.

  Language:Python3302