Alternatives and similar repositories for speciesprimer

Users that are interested in speciesprimer are comparing it to the libraries listed below

• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆22Updated 2 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆46Updated 2 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆72Updated 2 months ago
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆54Updated 5 years ago
• a-h-b / dadasnake
  Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
  ☆49Updated last year
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 3 years ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated 3 weeks ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆45Updated 5 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• EBI-Metagenomics / mettannotator
  ☆79Updated 2 weeks ago
• donovan-h-parks / RefineM
  A toolbox for improving metagenome-assembled genomes.
  ☆62Updated 4 years ago
• vinuesa / get_phylomarkers
  A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…
  ☆59Updated 9 months ago
• ohlab / GRiD
  Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …
  ☆31Updated 5 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆59Updated last year
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆64Updated last week
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆42Updated 5 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆62Updated 2 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• nvelden / geneviewer
  An R package designed for drawing gene arrow maps
  ☆91Updated last month
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆66Updated last year
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆61Updated 6 years ago
• functional-dark-side / agnostos-wf
  ☆45Updated 2 years ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆55Updated 3 years ago
• Microbial-Ecology-Group / AMRplusplus
  AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resis…
  ☆43Updated last month
• liaochenlanruo / pgcgap
  The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline
  ☆39Updated 2 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆46Updated last week
• Carrion-lab / bacLIFE
  ☆50Updated last month
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 6 months ago