Alternatives and similar repositories for PiRATE

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

• obenno / ShinySyn
  A shiny application to visualize MCscan result
  ☆37Updated 3 years ago
• clemgoub / dnaPipeTE
  dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…
  ☆59Updated 2 years ago
• ellenbell / FasTE
  A quick user guide for de novo transposable element (TE) library generation and TE screening. Utilising; the Extensive de novo TE Annotat…
  ☆27Updated 2 years ago
• annaprotasio / TE_ManAnnot
  Accompanying repository for our publications on manual curation methods for Transposable Elements.
  ☆21Updated last year
• dwinter / repeatR
  read and analyse RepeatMasker output
  ☆27Updated 2 years ago
• Yandell-Lab / maker
  Genome Annotation Pipeline
  ☆41Updated last year
• bergmanlab / TELR
  TELR is a fast non-reference transposable element detector from long read sequencing data.
  ☆35Updated 2 years ago
• schneebergerlab / AMPRIL-genomes
  scripts for the project of seven thaliana genomes assembly
  ☆42Updated 4 years ago
• johnssproul / RepeatProfiler
  ☆26Updated 9 months ago
• hillerlab / make_lastz_chains
  Portable solution to generate genome alignment chains using lastz
  ☆59Updated 2 months ago
• slimsuite / chromsyn
  Chromosome-level synteny plotting using orthologous regions
  ☆30Updated last year
• bcgsc / ntSynt-viz
  Multi-genome synteny block visualization tool
  ☆49Updated last month
• DrosophilaGenomeEvolution / TrEMOLO
  Transposable Elements MOvement detection using LOng reads
  ☆25Updated 4 months ago
• alachins / sweed
  Likelihood-based Selective Sweep Detection
  ☆40Updated 2 years ago
• INTABiotechMJ / MITE-Tracker
  MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes
  ☆20Updated last year
• drostlab / LTRpred
  De novo annotation of young retrotransposons
  ☆48Updated 3 years ago
• JanaSperschneider / FindTelomeres
  A python script for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files
  ☆35Updated 3 years ago
• akcorut / kGWASflow
  kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
  ☆43Updated last year
• HuffordLab / GenomeQC
  ☆33Updated 4 years ago
• phasegenomics / juicebox_scripts
  A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats
  ☆69Updated 4 years ago
• stevemussmann / admixturePipeline
  A pipeline that accepts a VCF file to run through Admixture
  ☆63Updated 10 months ago
• niccw / repeatcraftp
  meta-pipeline for repetitive element de-fragmentation and annotation
  ☆28Updated 5 years ago
• Gaius-Augustus / TSEBRA
  TSEBRA: Transcript Selector for BRAKER
  ☆48Updated 2 weeks ago
• mapleforest / HaploMerger2
  ☆45Updated 8 years ago
• heche-psb / wgd
  wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication
  ☆37Updated 9 months ago
• Farre-lab / syntenyPlotteR
  R package to draw syntenic plots in 3 different styles
  ☆42Updated 3 months ago
• phasegenomics / hic_qc
  A (very) simple script to QC Hi-C data.
  ☆26Updated 11 months ago
• sudmantlab / loco-pipe
  loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genom…
  ☆25Updated last month
• alachins / raisd
  RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
  ☆36Updated 2 years ago
• wjian8 / psvcp_v1.01
  Pan-genome Construction and Population Structure Variation Calling pipeline
  ☆44Updated last year