SilasK

Husband, Father & Metagenome researcher

Geneva

Pinned Repositories

atlas
ATLAS - Three commands to start analyzing your metagenome data
Language:Python379 15 43499
16S-dada2
Snakemake pipeline for amplicon sequencing using dada2
Language:Python9 2 67
Bubbleplot
Language:Jupyter Notebook1 2 00
FastDrep
Language:Python1 2 00
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Language:C++1 0 00
ipath3
Python wrapper for ipath3
Language:Jupyter Notebook10 3 11
Krak
Snakemake for flexitaxd and Kraken2
Language:Python6 4 33
stamps2019
Materials for the STAMPS 2019 course at the MBL in Woods Hole, MA, USA
Language:HTML2 1 00
statsplot
Language:Jupyter Notebook4 1 00

SilasK's Repositories

SilasK/stamps2019
Materials for the STAMPS 2019 course at the MBL in Woods Hole, MA, USA
Language:HTML2 1 00
SilasK/2018_scWorkshop
Language:R2 0
SilasK/abinner
Language:Python2 0
SilasK/andi
♥ Efficient Estimation of Evolutionary Distances
Language:C2 0
SilasK/BBMap
(Not Offical) BBMap short read aligner, and other bioinformatic tools.
Language:Java2 0
SilasK/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell2 0
SilasK/BioMetaDB
Use biological data to generate SQL database schema
Language:Python1 0
SilasK/bioservices
Access to Biological Web Services from Python.
Language:Python
SilasK/CoDaSeq
Functions for compositional analysis of high throughput sequencing
Language:R1 0
SilasK/cytoscape-automation
Collection of scripts that include programmatic io and control of Cytoscape
Language:HTML2 0
SilasK/DAS_Tool
DAS Tool
Language:Shell2 0
SilasK/drep
Rapid comparison and dereplication of genomes
Language:Python1 0
SilasK/eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
Language:Python1 0
SilasK/MAGpurify
Improvement of metagenome-assembled genomes
Language:Python
SilasK/MMprofiler
Create mmseq2 profiles from (unaligned) protein families/clusters, under development
Language:Python0 0
SilasK/MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
Language:C++2 01
SilasK/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
Language:Python1 01
SilasK/oldSRA_download
script for downloading files from sra
Language:Python
SilasK/pandas-formats-benchmark
A little benchmark comparing Pandas data frames serialization formats
Language:Jupyter Notebook0 0
SilasK/phigaro
Phigaro is a scalable command-line tool for predictions phages and prophages from nucleid acid sequences (including metagenomes) and is based on phage genes HMMs and a smoothing window algorithm.
SilasK/pygenprop
A python library for programmatic usage of EBI InterPro Genome Properties.
Language:Python2 0
SilasK/RNA-seq
Language:R2 0
SilasK/SCAPP
SCAPP is a plasmid assembly tool. A preprint describing this tool is available at: https://www.biorxiv.org/content/10.1101/2020.01.12.903252v1
Language:Python1 0
SilasK/spades
SPAdes Genome Assembler
Language:C++1 0
SilasK/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
Language:Python1 0
SilasK/surfsara-grid
This profile configures Snakemake to run on any cluster systems.
Language:Python
SilasK/table2itol
Generating iToL annotations from Spreadsheet or CSV files
Language:R0 0
SilasK/tax2tree
Automated taxonomy decoration onto a tree
SilasK/unige-thesistemplate
Language:TeX1 0
SilasK/viralVerify
viralVerify: viral contig verification tool
Language:Python1 0