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    19 repositories

    • somaticseq

      Public
      An ensemble approach to accurately detect somatic mutations using SomaticSeq
      somatic-variantscancer-genomics
      Python
      •
      BSD 2-Clause "Simplified" License
      •53•195•6•0•Updated Feb 7, 2025Feb 7, 2025

    • varsim

      Public
      VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
      validationgenomicssimulationhigh-throughput-sequencing
      Java
      •
      BSD 2-Clause "Simplified" License
      •31•81•36•5•Updated Oct 3, 2024Oct 3, 2024

    • SeqLib

      Public
      C++ htslib/bwa-mem/fermi interface for interrogating sequence data
      C++
      •
      Other
      •37•0•0•0•Updated Feb 4, 2023Feb 4, 2023

    • ichorCNA

      Public
      Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
      R
      •
      GNU General Public License v3.0
      •89•0•0•1•Updated Sep 22, 2022Sep 22, 2022

    • bwa

      Public
      Burrow-Wheeler Aligner for pairwise alignment between DNA sequences
      C
      •
      Apache License 2.0
      •554•1•0•0•Updated Jan 16, 2022Jan 16, 2022

    • fermi-lite

      Public
      Standalone C library for assembling Illumina short reads in small regions
      C
      •
      MIT License
      •23•0•0•0•Updated Jan 16, 2022Jan 16, 2022

    • Daedalus

      Public
      C++
      •
      Other
      •0•1•0•0•Updated Jan 6, 2022Jan 6, 2022

    • neusomatic

      Public
      NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
      deep-learninggenomicssomatic-variantsconvolutional-neural-networks
      Python
      •
      Other
      •50•168•22•8•Updated Dec 23, 2021Dec 23, 2021

    • swifr

      Public
      C++
      •
      Other
      •1•3•0•0•Updated Oct 25, 2021Oct 25, 2021

    • ecTMB

      Public
      cancer-genomicstmb
      R
      •
      Other
      •10•19•4•0•Updated Aug 22, 2021Aug 22, 2021

    • rnacocktail

      Public
      rna-seq
      Jupyter Notebook
      •
      Other
      •48•88•4•0•Updated Nov 11, 2020Nov 11, 2020

    • QBC_Single_Cell_Analysis_NGS

      Public
      C++
      •
      GNU General Public License v3.0
      •0•2•1•0•Updated Feb 3, 2020Feb 3, 2020

    • metasv

      Public
      MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
      Python
      •
      BSD 2-Clause "Simplified" License
      •21•55•29•2•Updated Jun 30, 2017Jun 30, 2017

    • longislnd

      Public
      LongISLND - Long In silico Sequencing of Lengthy and Noisy Datatypes
      Java
      •
      Other
      •4•4•3•0•Updated Apr 30, 2017Apr 30, 2017

    • IDP

      Public
      IDP is a statistical isoform prediction method to construct possible isoform candidates from the union of long reads and short reads with spliced alignment
      Python
      •
      Other
      •4•7•0•0•Updated Feb 23, 2017Feb 23, 2017

    • huref-gs

      Public
      0•1•0•0•Updated Feb 2, 2017Feb 2, 2017

    • breakseq2

      Public
      BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants
      Python
      •
      BSD 2-Clause "Simplified" License
      •5•24•7•0•Updated Mar 17, 2016Mar 17, 2016

    • LSC

      Public
      LSC is a long read error correction tool. It offers fast correction with high sensitivity and good accuracy.
      Python
      •
      Other
      •1•6•1•0•Updated Dec 10, 2014Dec 10, 2014

    • pindel

      Public
      Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
      C++
      •
      GNU General Public License v3.0
      •90•1•0•0•Updated Jun 20, 2014Jun 20, 2014