Adam Taranto

teloclip. A tool for the recovery of unassembled telomeres from soft-clipped read alignments.

TRF2GFF. Convert Tandem Repeat Finder dat file output into gff3 format

TIRmite. Annotation of cryptic transposon variants using Hidden Markov Models to detect conserved terminal features.

blast-besties. Rapid discovery of reciprocal best blast pairs.

Corset-tools. Companion scripts for annotation of Corset generated transcript clusters.

MITE_Hunter_2. Minor edits to allow MITE_Hunter (Han & Wessler 2010) to use modern blast+

frisk. Screen genomic scaffolds for regions of unusual k-mer composition.

GraphTagger. Small script to compute coverage of contigs from reads

TE-insertion-scanner. Scan whole genome alignments for signatures of transposon insertion.

maxiprot. Select best alignment from overlapping miniprot alignments

LTR-Harvest-Reformat. Correct sequence names in LTR_Harvest GFF3 output.

EarlGrey. Earl Grey: A fully automated TE curation and annotation pipeline

TEtrimmer. TEtrimmer: a novel tool to automate manual curation of transposable elements

density-Mapr. An R workflow for creating heat-maps representing the spatial association between two genomic feature sets

tSplit. Extract terminal repeats from retrotransposons (LTRs) or DNA transposons (TIRs). Compose synthetic MITES from complete DNA transposons.

Yanagiba. Filter and slice Nanopore reads which have been basecalled with Albacore.

bioconda-recipes. Conda recipes for the bioconda channel.

subset-fasta-by-name. Subset, split, and correct formatting of multiple sequence FASTA files.

TE-dispersion-metric. Proposed metric for measuring the clustering of transposons within a genome

mimeo. Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.