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