Repositories list

• svict

  Public
  Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA

  structural-variationliquid-biopsypaired-end-sequencing

  C++

  •

  BSD 3-Clause "New" or "Revised" License

  •6•25•14•0•Updated Jun 6, 2024Jun 6, 2024

• tksm

  Public
  Very modular, very cool long-read transcriptomic simulator

  C++

  •

  MIT License

  •0•5•4•1•Updated May 13, 2024May 13, 2024

• scTagger

  Public
  10x single cell short- and long-read RNA sequencing

  Python

  •

  MIT License

  •0•11•1•0•Updated Jan 17, 2024Jan 17, 2024

• calib

  Public
  Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.

  clusteringliquid-biopsytagged-reads+ 2barcode-sequencingpaired-end-sequencing

  HTML

  •

  MIT License

  •9•38•3•0•Updated Jun 6, 2023Jun 6, 2023

• genion

  Public
  GENe fusION

  C++

  •

  MIT License

  •1•7•2•0•Updated Jun 6, 2023Jun 6, 2023

• freddie

  Public
  Freddie: Annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing

  Python

  •

  MIT License

  •3•17•3•0•Updated Nov 29, 2022Nov 29, 2022

• sedef

  Public
  Identification of segmental duplications in the genome

  structural-variationsegmental-duplications

  C++

  •

  MIT License

  •8•26•0•0•Updated Mar 1, 2022Mar 1, 2022

• LTR-sim

  Public
  Long transcriptomic reads simulator

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 13, 2021Sep 13, 2021

• circminer

  Public
  A sensitive and fast tool for circular RNA detection from RNA-Seq data

  bioinformaticsrna-seqtranscriptomics+ 1circrna

  C++

  •

  GNU General Public License v3.0

  •4•10•4•0•Updated May 4, 2021May 4, 2021

• util-progressbar

  Public
  C++

  •

  MIT License

  •0•1•0•0•Updated Mar 24, 2021Mar 24, 2021

• pamir

  Public
  Discovery and Genotyping of Novel Sequence Insertions in Many Sequenced Individuals

  structural-variation

  C++

  •

  BSD 3-Clause "New" or "Revised" License

  •4•8•6•1•Updated Mar 22, 2021Mar 22, 2021

• util-logger

  Public
  C++

  •

  MIT License

  •0•0•0•0•Updated Apr 24, 2020Apr 24, 2020

• haslr

  Public
  A fast tool for hybrid genome assembly of long and short reads

  bioinformaticsnanoporegenomics+ 4pacbiogenome-assemblylong-readshybrid-assembly

  C++

  •

  GNU General Public License v3.0

  •9•76•29•0•Updated Apr 22, 2020Apr 22, 2020

• lordfast

  Public
  Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.

  mappinglong-readpacbio+ 2oxford-nanoporesingle-molecule-sequencing

  C

  •

  GNU General Public License v3.0

  •4•41•7•0•Updated Jul 15, 2019Jul 15, 2019

• lordfast-extra

  Public
  Contains extra information for lordFAST paper

  C++

  •1•0•0•0•Updated Apr 3, 2019Apr 3, 2019