Adamtaranto

followers

following

stars

The University of Melbourne

Melbourne, Australia

Organizations

bioconda

COMBINE-Canberra

Adam Taranto's repositories

teloclip

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

Language:PythonNOASSERTION33 5 22

TRF2GFF

Convert Tandem Repeat Finder dat file output into gff3 format

Language:PythonGPL-3.017 4 2

blast-besties

Rapid discovery of reciprocal best blast pairs.

Language:PythonMIT10 4 1

Corset-tools

Companion scripts for annotation of Corset generated transcript clusters.

Language:PythonGPL-2.08 4 1

TIRmite

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

Language:PythonNOASSERTION4 4 12

LTR-Harvest-Reformat

Correct sequence names in LTR_Harvest GFF3 output.

Language:PythonMIT2 3 1

bioconda-recipes

Conda recipes for the bioconda channel.

Language:ShellMIT1 30

mimeo

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

Language:PythonMIT1 30

subset-fasta-by-name

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

Language:PythonMIT1 3 1

TE-dispersion-metric

Proposed metric for measuring the clustering of transposons within a genome

Language:PythonMIT1 30

TE-insertion-scanner

Scan whole genome alignments for signatures of transposon insertion.

Language:PythonMIT1 3 1

TE-splitter

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

Language:PythonMIT1 30

Yanagiba

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

Language:PythonMIT1 3 1

deRIP2

Predict progenitor sequence of fungal repeat families by correcting for RIP-like mutations and cytosine deamination events. Mask RIP or deamination events from alignments.

Language:PythonMIT04 10

MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

Language:PythonNOASSERTION01 1

TE-Reunite

For a set of reference transposons, collect instances from one or more genomes. Use aligned collections to build models capturing TE family diversity or produce deRIP'd reference sequence.

Language:PythonMIT030

flo

Transfer annotations between genome assemblies using chained whole-genome alignment and UCSC LiftOver. Forked from wurmlab/flo.

Language:Ruby030

GraphTagger

Small script to compute coverage of contigs from reads

Language:PythonGPL-3.0010

GraphUnzip

Unzip assembly graphs with Hi-C data and/or long reads.

Language:PythonGPL-3.0010

hmmlearn

Hidden Markov Models in Python, with scikit-learn like API

Language:PythonBSD-3-Clause030

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

Language:PythonBSD-2-Clause030

low-mem-genomics

Low memory methods for genomic software development

GPL-3.0020

MpGAP

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

Language:NextflowGPL-3.0010

nbgrader-gitpod-template

Config scripts for managing nbgrader envs in Gitpod

Language:PythonGPL-3.0000

planets

Example git repo for wehi git intro course.

MIT020

RECONcile

Take clustered element fragment coordinates from RECON and write sequences to fasta for alignment and consensus calling.

Language:PythonMIT03 3

smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Language:RApache-2.0010

swc-shell-novice

The Unix Shell

Language:ShellNOASSERTION010

training-material

A collection of Galaxy-related training material

Language:HTMLMIT020

Transposon-Tools-List

A list of useful software tools for predicting, classifying, annotating, and analysing Transposable Elements.

GPL-3.0030