Alternatives and similar repositories for GAPIT

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

• BGI-shenzhen / LDBlockShow
  LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
  ☆185Updated last month
• BGI-shenzhen / PopLDdecay
  PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
  ☆194Updated last year
• xiaolei-lab / rMVP
  A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study
  ☆305Updated last month
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆313Updated 2 years ago
• TickingClock1992 / RIdeogram
  ☆179Updated 4 years ago
• showteeth / ggcoverage
  Visualize and annotate genomic coverage with ggplot2
  ☆261Updated 7 months ago
• JoniColeman / gwas_scripts
  Codebook from my GWAS cookbook
  ☆193Updated 3 years ago
• YuLab-SMU / MicrobiotaProcess
  A comprehensive R package for deep mining microbiome
  ☆191Updated last month
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆219Updated last month
• YongxinLiu / Note
  ☆125Updated 3 years ago
• YaoLab-Bioinfo / shinyCircos
  an R/shiny application for creation of Circos plot interactively
  ☆158Updated 2 years ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆142Updated 10 years ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆214Updated last year
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆114Updated 10 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆219Updated last month
• YongxinLiu / Metagenome
  Metagenome analysis pipeline
  ☆99Updated 4 years ago
• cafferychen777 / ggpicrust2
  Make Picrust2 Output Analysis and Visualization Easier
  ☆154Updated this week
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆338Updated 2 months ago
• wwood / kingfisher-download
  Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
  ☆274Updated last week
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆171Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆239Updated last month
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆269Updated last week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆239Updated 4 years ago
• hillerlab / TOGA
  TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…
  ☆191Updated 2 months ago
• nf-core / ampliseq
  Amplicon sequencing analysis workflow using DADA2 and QIIME2
  ☆213Updated last week
• hahnlab / CAFE
  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
  ☆117Updated 4 years ago
• taowenmicro / ggClusterNet
  Microbial ecological network visualization clustering
  ☆123Updated 5 months ago
• YongxinLiu / EasyMicrobiome
  ☆118Updated last month
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆141Updated last month
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆268Updated 8 months ago