kujawskm

kujawskm's Stars

• andland/logisticPCA

  Dimensionality reduction for binary data

  Language:HTML499

• gamcil/clinker

  Gene cluster comparison figure generator

  Language:Python51568

• widdowquinn/pyani

  Application and Python module for average nucleotide identity analyses of microbes.

  Language:Python19255

• iqtree/iqtree2

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

  Language:C++23155

• joey711/phyloseq

  phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

  Language:R577187

• oschwengers/bakta

  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

  Language:Python42651

• tseemann/barrnap

  :microscope: :leo: Bacterial ribosomal RNA predictor

  Language:Perl21740

• tseemann/snp-sites

  Finds SNP sites from a multi-FASTA alignment file

  Language:C5

• tseemann/prokka

  :zap: :aquarius: Rapid prokaryotic genome annotation

  Language:Perl809222

• tseemann/abricate

  :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

  Language:Perl36088

• jts/nanopolish

  Signal-level algorithms for MinION data

  Language:C++557160

• kblin/ncbi-genome-download

  Scripts to download genomes from the NCBI FTP servers

  Language:Python927176

• JCVI-metagenomics/SubDBer

  Flexible taxonomy-based subsampling of sequence database for efficient and focused metagenomic analyses

  Language:Python11

• richardmleggett/MARTi

  Metagenomic Analysis in Real Time

  Language:Java172

• AnantharamanLab/METABOLIC

  A scalable high-throughput metabolic and biogeochemical functional trait profiler

  Language:Perl17242

• DallasThomas/SACCHARIS

  Improve functional predictions of uncharacterized sequences for any CAZyme or CBM family

  Language:Perl64

• zellerlab/GECCO

  GEne Cluster prediction with COnditional random fields.

  Language:Python547

• MrOlm/drep

  Rapid comparison and dereplication of genomes

  Language:Python24536

• benjjneb/dada2

  Accurate sample inference from amplicon data with single nucleotide resolution

  Language:R459142

• linnabrown/run_dbcan

  Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

  Language:Python13840

• ACCLAB/dabestr

  Data Analysis with Bootstrap Estimation in R

  Language:R21434

• DRL/blobtools

  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

  Language:Python18644

• assemblerflow/flowcraft

  FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:

  Language:Python24144

• KasperSkytte/mmgenome2

  Tools for extracting individual genomes from metagenomes

  Language:R175

• sanger-pathogens/snp-sites

  Finds SNP sites from a multi-FASTA alignment file

  Language:C23350

• tseemann/snp-dists

  Pairwise SNP distance matrix from a FASTA sequence alignment

  Language:C12628

• tseemann/snippy

  :scissors: :zap: Rapid haploid variant calling and core genome alignment

  Language:Perl463113

• nickjcroucher/gubbins

  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

  Language:Python16649

• kwongj/maskrc-svg

  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG

  Language:Python186