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bam2fq

bam to fastq converter ui

cdna_cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

controldna

is a bioinformatics best-practice analysis pipeline for alignment for our control DNA

fadapa

FAstqc DAta PArser - A minimal parser to parse FastQC output data.

fastqc

csf fork of fastqc for usage on selected reads of unaligned bam file

forskalle-api

Command Line Interface and Python API for Forskalle

forskaller

simple small API for our superior in house LIMS built by Heinz

hinkskalle

OCI + Singularity Container Registry

hinkskalle-api

Talking to Hinkskalle

hinkskalle-dev

Development Container for Hinkskalle

illumina2bam

illuminabackup

small backup program that copies the important files from illumina sequencing runs

illuminasavr

Parses and Plots Illumina SAV files

metrix

A Server / Client parser for Illumina InterOp sequencer run metrics written in Java 7.0.

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

sga

de novo sequence assembler using string graphs

sqanti2

Private repo for Liz's modified SQANTI

surecellumi

extraction of Illumina SureCell UMI protocol. Compatible with umi-tools

swagspotta

Generate typescript + python classes from Swagger/OpenAPI 2 definitions