Peter Kruczkiewicz's repositories
bioconda-recipes
Conda recipes for the bioconda channel.
2024-05-06-ASFV-NC_044954.1-phold-annotation
pharokka and phold annotation of ASFV genome NC_044954.1
cobra
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
TreeOrdination
Creating and analyzing projections created from decision tree ensembles.
LANDMark
Implementation of a decision tree ensemble which splits each node using learned linear and non-linear functions.
runscanner
Monitors directories on the file system containing the output from sequencing instruments (e.g. Illumina) and reports their status and metrics
guppywuppy
Basic service wrapping PyGuppyClient talking to fast5watch
vcf_consensus_builder
Build a consensus sequence from a VCF and reference sequence masking low and no coverage positions
filter_classified_reads
Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.
sublime-nextflow
Nextflow workflow syntax highlighting and snippets for Sublime Text 4
nf-villumina
Generic viral Illumina sequence analysis pipeline
nf-test-datasets
Nextflow workflow test datasets for CI
fasta2lmdb
Quickly save FASTA sequences to an LMDB key-value database for rapid retrieval.
longshot
diploid SNV caller for error-prone reads
bertax
Taxonomic classification of DNA sequences
multi-package-containers
Testing building mulled containers for multi-requirement tools.
nf-core-tools
Python package with helper tools for the nf-core community.
package_control_channel
Default channel file for Package Control. Follow the directions at:
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
miso-lims
MISO: An open-source LIMS for NGS sequencing centres