raufs

raufs's Stars

• broadinstitute/gatk

  Official code repository for GATK versions 4 and up

  Language:Java1.7k1544.6k597

• broadinstitute/picard

  A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

  Language:Java990157807371

• YuLab-SMU/ggtree

  :christmas_tree:Visualization and annotation of phylogenetic trees

  Language:R85038506173

• bwa-mem2/bwa-mem2

  The next version of bwa-mem

  Language:C++72736214102

• stamatak/standard-RAxML

  Language:C3324954193

• wwood/CoverM

  Read coverage calculator for metagenomics

  Language:Rust3111116731

• kcleal/gw

  Genome browser and variant annotation

  Language:C++2876247

• lmdu/pyfastx

  a python package for fast random access to sequences from plain and gzipped FASTA/Q files

  Language:C27077123

• iqtree/iqtree2

  NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

  Language:C++2581524358

• wwood/kingfisher-download

  Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

  Language:Python25173438

• CAMI-challenge/CAMISIM

  CAMISIM: Simulating metagenomes and microbial communities

  Language:Python1852318937

• rrwick/Long-read-assembler-comparison

  Benchmarking of long-read assembly tools for bacterial whole genomes

  Language:Python17014414

• steineggerlab/foldmason

  Multiple Protein Structure Alignment at Scale with FoldMason

  Language:C14451214

• qiyunlab/HGTector

  HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

  Language:Python131109335

• snayfach/MIDAS

  An integrated pipeline for estimating strain-level genomic variation from metagenomic data

  Language:Python124129452

• althonos/peptides.py

  Physicochemical properties, indices and descriptors for amino-acid sequences.

  Language:Python766412

• emmanuelparadis/ape

  Analysis of Phylogenetics and Evolution

  Language:R5777311

• jlw-ecoevo/gRodon2

  Language:R403134

• morgannprice/PaperBLAST

  PaperBLAST: find papers about a protein or its homologs

  Language:Perl372186

• czbiohub-sf/MIDAS

  Metagenomic Intra-Species Diversity Analysis (MIDAS)

  Language:Python3663910

• emmanuelparadis/pegas

  Population and Evolutionary Genetics Analysis System

  Language:R2968110

• Ebedthan/xgt

  Efficient and fast querying and parsing of GTDB's data

  Language:Rust28110

• zjshi/gt-pro

  Language:C++233387

• Kalan-Lab/lsaBGC-Pan

  lsaBGC - suite for pan-BGC-omics analysis

  Language:Python18292

• EBI-Metagenomics/kegg-pathways-completeness-tool

  Language:Python15723

• pablocael/pynear

  A python library for efficient KNN search within metric spaces using multiple distance functions.

  Language:C++133183

• bsmith89/StrainFacts

  Factorize metagenotypes to infer strains and their abundances

  Language:Python113141

• Ebedthan/hkgfinder

  Find housekeeping genes in prokaryotic (meta)genomic data

  Language:Python11100

• Kalan-Lab/codoff

  codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.

  Language:Python11201

• Kalan-Lab/Bioassay-ML-Image-Classification

  This repository contains a script for training a machine learning model to classify images into categories. The model is trained on custom images provided by the user.

  Language:Jupyter Notebook1200