Adamtaranto/TE-splitter

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Language
Python
License
MIT License
Created over 7 years ago
Updated about 7 years ago

Adamtaranto/TE-splitter

Adamtaranto

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

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

Corset-tools

Companion scripts for annotation of Corset generated transcript clusters.

blast-besties

Rapid discovery of reciprocal best blast pairs.

TIRmite

Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.

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.

LTR-Harvest-Reformat

Correct sequence names in LTR_Harvest GFF3 output.

subset-fasta-by-name

Subset, split, and correct formatting of multiple sequence FASTA files.

density-Mapr

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

mimeo

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

HowToScience

A knowledge engine for new students of bioinformatics.

TE-insertion-scanner

Scan whole genome alignments for signatures of transposon insertion.