kujawskm's Stars
andland/logisticPCA
Dimensionality reduction for binary data
gamcil/clinker
Gene cluster comparison figure generator
widdowquinn/pyani
Application and Python module for average nucleotide identity analyses of microbes.
iqtree/iqtree2
NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
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:
oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
tseemann/barrnap
:microscope: :leo: Bacterial ribosomal RNA predictor
tseemann/snp-sites
Finds SNP sites from a multi-FASTA alignment file
tseemann/prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
jts/nanopolish
Signal-level algorithms for MinION data
kblin/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
JCVI-metagenomics/SubDBer
Flexible taxonomy-based subsampling of sequence database for efficient and focused metagenomic analyses
richardmleggett/MARTi
Metagenomic Analysis in Real Time
AnantharamanLab/METABOLIC
A scalable high-throughput metabolic and biogeochemical functional trait profiler
DallasThomas/SACCHARIS
Improve functional predictions of uncharacterized sequences for any CAZyme or CBM family
zellerlab/GECCO
GEne Cluster prediction with COnditional random fields.
MrOlm/drep
Rapid comparison and dereplication of genomes
benjjneb/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
linnabrown/run_dbcan
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
ACCLAB/dabestr
Data Analysis with Bootstrap Estimation in R
DRL/blobtools
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
assemblerflow/flowcraft
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:
KasperSkytte/mmgenome2
Tools for extracting individual genomes from metagenomes
sanger-pathogens/snp-sites
Finds SNP sites from a multi-FASTA alignment file
tseemann/snp-dists
Pairwise SNP distance matrix from a FASTA sequence alignment
tseemann/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
nickjcroucher/gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
kwongj/maskrc-svg
Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG