SciLifeLab/software-development

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SciLifeLab/software-development

SciLifeLab

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General guidelines and style guide for software developed at SciLifeLab

TIDDIT

TIDDIT - structural variant calling

facs

Fast and Accurate Classification of Sequences using Bloom filters

Jupyter Notebook

genomics-status

Tornado server for tracking samples at NGI Stockholm

NGI-CellRaiser

Pipeline for analysing 10X single cell data

flowcell_parser

Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output

umi-transfer

A Rust software to extract Unique Molecular Identifiers in FastQ files and embedd them into the ID of the corresponding reads.

NGI-NextflowDocs

Common documentation for National Genomics Infrastructure pipelines built with Nextflow

standalone_scripts

Repository to store standalone scripts that do not belong to any bigger package or repository

gapest

Reference implementation of the scaffolding gap size estimation algorithm by Kristoffer Sahlin

CAW-containers

Containers for CAW

internal-provisioning

Ansible repository for deployment stuff

genomics-dashboard

dotfiles

statusdb

Python wrappers and methods to work with CouchDB's instance at NGI Stockholm

scilifelab.github.io

Web portal for open source (research) projects at SciLifeLab

modules.sf.net

Adhoc software "packaged" for the ancient and deprecated "module system" (http://modules.sf.net/)

scilifelab_parsers

Module for scilifelab parsers of metrics and other files

slog

simple lab logging system

portal

SciLifeLab Genomics Customer Portal