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    19 repositories

    • forskalle-api

      Public
      Command Line Interface and Python API for Forskalle
      Python
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • controldna

      Public
      is a bioinformatics best-practice analysis pipeline for alignment for our control DNA
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • swagspotta

      Public
      Generate typescript + python classes from Swagger/OpenAPI 2 definitions
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 4, 2025Oct 4, 2025

    • hinkskalle

      Public
      OCI + Singularity Container Registry
      dockerregistryserver
      dockerregistryserversingularityocioras
      Python
      •
      MIT License
      •1•8•10•1•Updated Jan 25, 2023Jan 25, 2023

    • hinkskalle-dev

      Public
      Development Container for Hinkskalle
      Dockerfile
      •0•0•0•0•Updated Oct 17, 2022Oct 17, 2022

    • hinkskalle-api

      Public
      Talking to Hinkskalle
      Python
      •
      MIT License
      •1•0•0•0•Updated May 6, 2022May 6, 2022

    • forskaller

      Public
      simple small API for our superior in house LIMS built by Heinz
      R
      •
      GNU General Public License v2.0
      •0•1•0•0•Updated Apr 24, 2022Apr 24, 2022

    • rnaseq

      Public
      RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
      Nextflow
      •
      MIT License
      •881•0•0•0•Updated May 13, 2021May 13, 2021

    • SQANTI2

      Public
      Private repo for Liz's modified SQANTI
      Python
      •
      Other
      •16•0•0•0•Updated Apr 8, 2019Apr 8, 2019

    • cDNA_Cupcake

      Public
      Miscellaneous collection of Python and R scripts for processing Iso-Seq data
      Python
      •
      BSD 3-Clause Clear License
      •106•0•0•0•Updated Mar 28, 2019Mar 28, 2019

    • illuminasavr

      Public
      Parses and Plots Illumina SAV files
      JavaScript
      •
      GNU General Public License v2.0
      •1•13•1•0•Updated Jan 30, 2019Jan 30, 2019

    • illuminaBackup

      Public
      small backup program that copies the important files from illumina sequencing runs
      Scala
      •1•2•1•0•Updated Jun 13, 2018Jun 13, 2018

    • surecellumi

      Public
      extraction of Illumina SureCell UMI protocol. Compatible with umi-tools
      Python
      •0•1•3•0•Updated Aug 30, 2017Aug 30, 2017

    • bam2fq

      Public
      bam to fastq converter ui
      Java
      •0•1•0•0•Updated Aug 3, 2016Aug 3, 2016

    • illumina2bam

      Public
      Java
      •15•0•0•0•Updated Jan 15, 2016Jan 15, 2016

    • fadapa

      Public
      FAstqc DAta PArser - A minimal parser to parse FastQC output data.
      Python
      •11•0•0•0•Updated Mar 3, 2015Mar 3, 2015

    • Metrix

      Public
      A Server / Client parser for Illumina InterOp sequencer run metrics written in Java 7.0.
      Java
      •
      Other
      •5•0•0•0•Updated Jun 17, 2013Jun 17, 2013

    • sga

      Public
      de novo sequence assembler using string graphs
      C++
      •81•0•0•0•Updated Mar 12, 2013Mar 12, 2013

    • fastqc

      Public
      csf fork of fastqc for usage on selected reads of unaligned bam file
      Java
      •
      GNU General Public License v3.0
      •40•49•0•0•Updated Mar 7, 2013Mar 7, 2013
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