Alternatives and similar repositories for TE-Seq

Users that are interested in TE-Seq are comparing it to the libraries listed below

• OliveiraDS-hub / ChimeraTE
  A pipeline to detect chimeric transcripts derived from genes and transposable elements.
  ☆27Updated this week
• AnimalGenomicsETH / bovine-graphs
  Integrate multiple genome assemblies into a pangenome graph
  ☆34Updated 2 years ago
• dwinter / repeatR
  read and analyse RepeatMasker output
  ☆24Updated last year
• clemgoub / rm2gff3
  Convert RepeatMasker ".out" file into a gff3 with colors!!!
  ☆21Updated 4 years ago
• IGDRion / ANNEXA
  Nextflow pipeline to extend reference annotation with nanopore reads, classify novel genes (mRNAs vs lncRNAs).
  ☆13Updated last month
• FAANG / analysis-TAGADA
  GENE-SWitCH project RNA-Seq analysis pipeline
  ☆25Updated 2 months ago
• sanger-tol / yahs
  Yet another Hi-C scaffolding tool
  ☆19Updated 6 months ago
• DessimozLab / OMAnnotator
  Consensus genome annotation using OMA
  ☆24Updated 2 weeks ago
• evotools / nf-LO
  A Nextflow workflow to generate lift over files for any pair of genomes
  ☆65Updated last month
• DrosophilaGenomeEvolution / TrEMOLO
  Transposable Elements MOvement detection using LOng reads
  ☆21Updated last week
• cfarkas / annotate_my_genomes
  A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes
  ☆29Updated last year
• agshumate / LiftoffTools
  ☆27Updated last year
• schatzlab / crossstitch
  Code for phasing SVs with SNPs
  ☆52Updated 5 years ago
• human-pangenomics / hprc-tutorials
  ☆17Updated last year
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆41Updated last year
• glarue / reciprologs
  Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.
  ☆13Updated 11 months ago
• lorrainea / CNEFinder
  CNEFinder: Finding Conserved Non-coding Elements in Genomes
  ☆23Updated 3 years ago
• almeidasilvaf / doubletrouble
  An R package to identify and classify duplicated genes from whole-genome protein sequence data
  ☆26Updated last month
• lh3 / calN50
  Compute N50/NG50 and auN/auNG
  ☆32Updated last year
• LAILAB-CAU / update-Mo17
  ☆24Updated 2 years ago
• bergmanlab / TELR
  TELR is a fast non-reference transposable element detector from long read sequencing data.
  ☆33Updated last year
• multiz / multiz
  DNA multiple sequence aligner, official version from Penn State's Miller Lab
  ☆32Updated 6 years ago
• hahnlab / CAGEE
  Computational Analysis of Gene Expression Evolution
  ☆40Updated last month
• eswlab / orphan-prediction
  methods for orphan gene prediction paper optimization
  ☆25Updated 3 years ago
• Rinoahu / SwiftOrtho
  A high performance tool to identify orthologs and paralogs across genomes.
  ☆26Updated 2 years ago
• PacificBiosciences / MethBat
  A battery of methylation tools for PacBio HiFi reads
  ☆34Updated 2 months ago
• maickrau / ribotin
  ☆32Updated this week
• vgteam / sv-genotyping-paper
  ☆30Updated 5 years ago
• mkirsche / Iris
  A module for improving the insertion sequences of structural variant calls
  ☆30Updated 3 years ago
• chenym1 / genetribe
  A tool for performing collinearity-incorporating homology inference
  ☆31Updated last year