ndombrowski
Postdoctoral scientist interested in obscure microbes and using sequencing data to study uncultured archaea
ndombrowski's Stars
katerinakazantseva/strainy
Graph-based assembly phasing
art-egorov/lovis4u
Bioinformatics tool for Locus Visualisation
nextgenusfs/funannotate
Eukaryotic Genome Annotation Pipeline
epi2me-labs/pychopper
cDNA read preprocessing
yfukasawa/LongQC
LongQC is a tool for the data quality control of the PacBio and ONT long reads.
ml4bio/Dense-Homolog-Retrieval
Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval
raw-lab/MetaCerberus
Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data
vsbuffalo/bds-files
Supplementary files for my book, "Bioinformatics Data Skills"
EBI-Metagenomics/mettannotator
weisberglab/beav
BEAV: Bacterial Element Annotation reVamped
lbcb-sci/herro
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
AnantharamanLab/VIBRANT
Virus Identification By iteRative ANnoTation
bpucker/teaching
This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.
andyposbe/ColabFold-Pipeline-Toolkit
The aim of this repository is to provide simple tools to help those working with ColabFold BATCH both for pre and post-processing steps.
wwood/CoverM
Read coverage calculator for metagenomics
Lafond-LapalmeJ/MCSC_Decontamination
Scripts and documentations on the MCSC decontamination method
smithlabcode/falco
A C++ drop-in replacement of FastQC to assess the quality of sequence read data
nf-core/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
bpucker/AppliedGenomeResearch
course about NGS data processing: genomics and transcriptomics
vsbuffalo/scidataflow
Command line scientific data management tool
Kinggerm/GetOrganelle
Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)
mdsufz/MuDoGeR
MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.
AlexanderLabWHOI/EukHeist
OpenGene/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
aquaskyline/SOAPdenovo-Trans
SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.
aquaskyline/SOAPdenovo2
Next generation sequencing reads de novo assembler.
jerry-git/learn-python3
Jupyter notebooks for teaching/learning Python 3
cxli233/Online_R_learning
Online R learning for applied statistics
zyxue/ncbitax2lin
🐞 Convert NCBI taxonomy dump into lineages
AADavin/ALEtutorial
A tutorial on Phylogenetic Reconciliations using ALE