Alternatives and similar repositories for LTR_retriever:

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

• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆218Updated 2 months ago
• hewm2008 / NGenomeSyn
  Any Way to Show Multi genomic Synteny
  ☆176Updated 4 months ago
• tangerzhang / ALLHiC
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆174Updated 4 months ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆197Updated last year
• PASApipeline / PASApipeline
  PASA software
  ☆184Updated last month
• huangnengCSU / compleasm
  A genome completeness evaluation tool based on miniprot
  ☆192Updated this week
• SunPengChuan / wgdi
  WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
  ☆134Updated 2 months ago
• mahulchak / quickmerge
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆205Updated 2 years ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 3 years ago
• BGI-Qingdao / TGS-GapCloser
  A gap-closing software tool that uses long reads to enhance genome assembly.
  ☆199Updated 6 months ago
• aaranyue / quarTeT
  A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
  ☆120Updated last month
• Dfam-consortium / RepeatModeler
  De-Novo Repeat Discovery Tool
  ☆205Updated 2 months ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆201Updated 2 years ago
• dfguan / purge_dups
  haplotypic duplication identification tool
  ☆227Updated last year
• zhangrengang / TEsorter
  TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
  ☆91Updated last month
• MariaNattestad / Assemblytics
  Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference gen…
  ☆140Updated 4 months ago
• baoxingsong / AnchorWave
  Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
  ☆166Updated 4 months ago
• xiaochuanle / NECAT
  Nanopore data assembler
  ☆143Updated 2 years ago
• hahnlab / CAFE
  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
  ☆116Updated 3 years ago
• hahnlab / CAFE5
  Version 5 of the CAFE phylogenetics software
  ☆127Updated last month
• ruanjue / smartdenovo
  Ultra-fast de novo assembler using long noisy reads
  ☆132Updated 4 years ago
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆176Updated last week
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆207Updated 2 weeks ago
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆183Updated last year
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆183Updated 9 months ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆143Updated last year
• linzhi2013 / MitoZ
  MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
  ☆120Updated 4 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆247Updated 4 months ago
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆159Updated last year
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆250Updated 2 months ago