Changwanseo

Multi-Type-TD-TSR

Extracting Tables from Document Images using a Multi-stage Pipeline for Table Detection and Table Structure Recognition:

TeloVision

Determine presence of telomeres and visualise genome assembly scaffolds.

Gooey

Turn (almost) any Python command line program into a full GUI application with one line

RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

jiffy-infernal-hmmer-scripts

Simple perl scripts for dealing with infernal and/or hmmer output/input.

CMPP

Annotate C(CAZy)M(MEROPS)P(PHI)P(P450) for fungi.

RoseTTAFold

This package contains deep learning models and related scripts for RoseTTAFold

uncalled4

TOUCAN

Supervised learning for fungal BGC discovery

RL-bgc-components

Reinforcement learning for improving components in fungal BGCs

LOCOM

A logistic regression model for testing differential abundance in compositional microbiome data

compare_genomes

A comparative genomics workflow using Nextflow, conda, Julia and R

python-mibig

Python handling of MIBiG data

DendroNet

Supervised learning on phylogeneticallydistributed data

unicore

Universal and efficient core gene phylogeny with Foldseek and ProstT5

quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

deepbgc

BGC Detection and Classification Using Deep Learning

PECAT

PECAT, a phased error correct and assembly tool

Hairsplitter

Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.

verkko

ntLink

Minimizer-based assembly scaffolding and mapping using long reads

goldrush

Linear-time de novo Long Read Assembler

HyLight

HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NGS and 3rd generation sequencing to rapidly and accurately assemble highly complex metagenomic sequencing data.

CrossHyLight

CrossHyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NGS and 3rd generation sequencing to rapidly and accurately assemble highly complex metagenomic sequencing data.

nQuire

A statistical framework for ploidy estimation using NGS short-read data

KEGGCharter

A tool for representing genomic potential and transcriptomic expression into KEGG pathways

Mabs

Mabs, a genome assembly tool which optimizes parameters of Hifiasm and Flye

tinycov

Command line tool to plot genomic coverage from a BAM file

whatshap

Read-based phasing of genomic variants, also called haplotype assembly