alneberg

vue-smart-suggest

Lightweight (<3KB) vue library offering context-sensitive suggestions in your textareas

nallo

A long-read (PacBio and ONT) analysis pipeline written in Nextflow

cruft

Allows you to maintain all the necessary cruft for packaging and building projects separate from the code you intentionally write. Built on-top of, and fully compatible with, CookieCutter.

MetaCC

MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data

umi-transfer

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

git-pa-svenska

Git på svenska

singularity-in-docker

A small repository with instructions on how to build Singularity images inside a Docker container.

git-history

Quickly browse the history of a file from any git repository

line_profiler

Line-by-line profiling for Python

dds_cli

The command line interface for access to the Data Delivery System primarily developed by the SciLifeLab Data Centre.

dds_web

A cloud-based system for the delivery of data from SciLifeLab Facilities to their users (e.g. research group).

couchdb-python

Python library for working with CouchDB

bioexcel

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

polar-rcx5-datalink

Command-line program to export Polar RCX5 training sessions or upload them to Strava

vamb

Variational autoencoder for metagenomic binning

ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

ngipubs

Web tool to find and annotate NGI publications

cookiecutter-pylibrary

Enhanced cookiecutter template for Python libraries.

cupper

Update cookiecutter projects

patterns

A curated collection of Nextflow implementation patterns

planets

drep

Rapid comparison and dereplication of genomes

EukRep

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

FastANI

Fast Whole-Genome Similarity (ANI) Estimation

GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

cdbfasta

Constant DataBase tools for indexing and retrieving records from multi-FASTA or similarly structured files

gattaca-public

Lightweight metagenomic binning

EMBLmyGFF3

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data