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/anglerfish
Codename: Anglerfish
alneberg/benchmark_demultiplexing
Some scripts to benchmark demultiplexing on our NGI infrastructure
alneberg/command_line_tips_and_tricks
A presentation of some useful tips and tricks
alneberg/conv_scripts
Convenient scripts to have around different places
alneberg/DailyRead
The NGI Daily Read
alneberg/docs_spider
Hopefully create a web of documents from our internal system
alneberg/fastapi_playground
Just learning fastapi
alneberg/flowcell_parser
Collection of python scripts to parse Illumina (demux with bcl2fastq v2.17+) output
alneberg/home_storage
Hobby project to keep track of things
alneberg/LIMS2DB
alneberg/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
alneberg/nextflow_playground
Started with the Nextflow Training session offered by nf-core
alneberg/NGI_dashboards
SciLifeLab NGI Dashboard Code
alneberg/ngi_reports
Code to generate reports for use by the NGI in SciLifeLab
alneberg/parasail_alignment
Mostly a playground to generate and compare parasail alignments
alneberg/rust_playground
Just playing around with rust
alneberg/scilifelab_epps
A collection of Genologics Clarity LIMS EPPs used at Scilifelab.
alneberg/seqinspector
(hopefully nf-core) pipeline to inspect your sequences
alneberg/spectacles
API for a clearer look at clarity
alneberg/standalone_scripts
Repository to store standalone scripts that do not belong to any bigger package or repository
alneberg/status
alneberg/statusdb
Python wrappers and methods to work with CouchDB's instance at NGI Stockholm
alneberg/StatusDB_tracer
Attempting to document which StatusDB views are used with static code analysis
alneberg/TACA
Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm
alneberg/taca-ngi-pipeline
A TACA plugin adding functionality relevant for the ngi_pipeline
alneberg/TankYou
Small hobby app to track cbg/cng mileage
alneberg/test-datasets
Test data to be used for automated testing with the nf-core pipelines
alneberg/trigger_error_nf
A dummy pipeline to attempt to trigger local issue with nextflow
alneberg/umi-injector
umi-injector integrates UMI sequences from a separate FastQ file into the read headers of a single or paired FastQ.
alneberg/umi-transfer
A Rust software to extract Unique Molecular Identifiers in FastQ files and embedd them into the ID of the corresponding reads.