Pinned Repositories
2015-04-BARM-Concoct
Running concoct for BARM using snakemake
alneberg
pythonkurs
alneberg.com
Personal (family) web page source code
alneberg.github.io
Personal Blog
anglerfish
Codename: Anglerfish
bu
Bioinformatic Utilities
DWUIR
Demultiplexing With UMIs in the Index Read
CONCOCT
Clustering cONtigs with COverage and ComposiTion
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
genomics-status
Tornado server for tracking samples at NGI Stockholm
alneberg's Repositories
alneberg/Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome sequencing data
alneberg/CONCOCT
Clustering cONtigs with COverage and ComposiTion
alneberg/ngi_pipeline
Code driving the production pipeline at SciLifeLab
alneberg/OrderPortal
A portal for orders (requests, project applications, etc) to a facility from its users.
alneberg/dds_cli
API to access Scilifelab Data Centre's delivery portal. On development
alneberg/dds_web
A cloud-based system for the delivery of data from SciLifeLab Facilities to their users (e.g. research group).
alneberg/ngisweden.se
Wordpress theme and plugins for ngisweden.se
alneberg/miarka-provision
Ansible playbooks for provisioning NGI cluster Miarka
alneberg/home_page_react
Trying out a personal react page
alneberg/BARM_web_server
Baltic sea Reference Metagenome web server
alneberg/FastAPI_demo
Just trying out FastAPI for the first time
alneberg/nf-co.re
Files for the main nf-core website >>>
alneberg/nextflow
A DSL for data-driven computational pipelines
alneberg/lims_dashboard
alneberg/genologics
Python interface to the GenoLogics LIMS server via its REST API.
alneberg/genologics_sql
Python interface for the Genologics Postgres database.
alneberg/bu
Bioinformatic Utilities
alneberg/irma-provision
Ansible playbooks for provisioning NGI pipeline and related sw
alneberg/personal_use
Scripts use for non-professional use
alneberg/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
alneberg/nanoseq
UNDER CONSTRUCTION: Nanopore demultiplexing, QC and alignment pipeline.
alneberg/bioconda-recipes
Conda recipes for the bioconda channel.
alneberg/configs
Config files used to define parameters specific to compute environments at different Institutions.
alneberg/DWUIR
Demultiplexing With UMIs in the Index Read
alneberg/garden
Pet project to manage garden duties and practice programming
alneberg/Sarek-data
Sarek test data and references
alneberg/MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
alneberg/mag
UNDER CONSTRUCTION: Assembly, binning and annotation of metagenomes.
alneberg/ngipubs
Web tool to find and annotate NGI publications
alneberg/strain_hackathon
Cost hackathon