Fredrik Boulund's repositories
measures
Contains implementation of various quantitative measures
metagenome_pipeline
A fairly standard metagenomics pipeline implemented in Nextflow.
proGenomes_scripts
Utility scripts for working with proGenomes
Bracken
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
ctmr_biopsies_test
Testing various taxonomic profiling approaches to simulated biopsy metagenomes
armen
Antibiotic Resistance in Metagenomes
MicrobeCensus
MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
scikit-bio
scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
wellness_filter_rows_columns
Small script to filter rows/columns from large tab-separated tables
IGC_taxonomy
Determine taxonomy for genes in IGC
wellness_wgs
Workflow for analysis of metagenomic samples within the SCAPIS Wellness project
extract_columns_from_lmed_data
Extract subset of columns from massive sas7bdat files
MultiQC_bbmap
BBMap module for MultiQC
Amplicon_workflows
Workflows and scripts for amplicon sequencing processing
coderefinery-travis-coveralls
testrepo for travisci and coverallsÂ
merge_taxonomic_classifications
Merge Kaiju, Kraken, and CLARK-S classifications of metagenomic reads
daisy
Horizontal Gene Transfer Detection by Mapping Sequencing Reads
testsajt
Testsajt