Pinned Repositories
bioconda-recipes
Conda recipes for the bioconda channel.
blast-besties
Rapid discovery of reciprocal best blast pairs.
Corset-tools
Companion scripts for annotation of Corset generated transcript clusters.
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.
frisk
Screen genomic scaffolds for regions of unusual k-mer composition.
LTR-Harvest-Reformat
Correct sequence names in LTR_Harvest GFF3 output.
MITE_Hunter_2
Minor edits to allow MITE_Hunter (Han & Wessler 2010) to use modern blast+
teloclip
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
TIRmite
Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.
TRF2GFF
Convert Tandem Repeat Finder dat file output into gff3 format
Adamtaranto's Repositories
Adamtaranto/teloclip
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
Adamtaranto/TRF2GFF
Convert Tandem Repeat Finder dat file output into gff3 format
Adamtaranto/blast-besties
Rapid discovery of reciprocal best blast pairs.
Adamtaranto/Corset-tools
Companion scripts for annotation of Corset generated transcript clusters.
Adamtaranto/TIRmite
Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.
Adamtaranto/LTR-Harvest-Reformat
Correct sequence names in LTR_Harvest GFF3 output.
Adamtaranto/bioconda-recipes
Conda recipes for the bioconda channel.
Adamtaranto/mimeo
Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.
Adamtaranto/TE-dispersion-metric
Proposed metric for measuring the clustering of transposons within a genome
Adamtaranto/TE-insertion-scanner
Scan whole genome alignments for signatures of transposon insertion.
Adamtaranto/Yanagiba
Filter and slice Nanopore reads which have been basecalled with Albacore.
Adamtaranto/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.
Adamtaranto/MitoFinder
MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
Adamtaranto/dev-sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
Adamtaranto/git-workshop-aug
Intro to git unimelb Aug 2024
Adamtaranto/GraphTagger
Small script to compute coverage of contigs from reads
Adamtaranto/GraphUnzip
Unzip assembly graphs with Hi-C data and/or long reads.
Adamtaranto/hmmlearn
Hidden Markov Models in Python, with scikit-learn like API
Adamtaranto/jcvi
Python utility libraries on genome assembly, annotation and comparative genomics
Adamtaranto/low-mem-genomics
Low memory methods for genomic software development
Adamtaranto/MpGAP
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
Adamtaranto/nbgrader-gitpod-template
Config scripts for managing nbgrader envs in Gitpod
Adamtaranto/planets
Example git repo for wehi git intro course.
Adamtaranto/python-novice-dataframes
Working with tabular data in Python
Adamtaranto/python-novice-inflammation
Programming with Python
Adamtaranto/smudgeplot
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Adamtaranto/student-gitpod-template
A template repo for students to work on coding workshops in Gitpodpod Workspace with Conda package management..
Adamtaranto/swc-shell-novice
The Unix Shell
Adamtaranto/training-material
A collection of Galaxy-related training material
Adamtaranto/Transposon-Tools-List
A list of useful software tools for predicting, classifying, annotating, and analysing Transposable Elements.