eernst

piler-64

Support for large memory allocations for the genomic repeat analysis tool from Robert Edgar and Eugene Myers.

BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

canu

A single molecule sequence assembler for genomes large and small.

catseq

Comparative-Annotation-Toolkit

EDTA

Extensive de-novo TE Annotator

Fastool

Simple and quick FastQ and FastA tool for file reading and conversion

Finder

A fully automated gene annotator from RNA-Seq expression data

finishingTool

finshingTool

Flye

De novo assembler for single molecule sequencing reads using repeat graphs

GENESPACE

homebrew-science

:microscope: Scientific formulae for the Homebrew package manager

IterativeErrorCorrection

Iterative error correction of long reads

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

kallisto

Near optimal RNA-Seq quantification

LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

NA12878

Data and analysis for NA12878 genome on nanopore

nanonet

First generation RNN basecaller

nanopolish

Signal-level algorithms for MinION data

nanoraw

Genome guided re-segmention and visualization for raw nanopore sequencing data.

ngmlr

Ngmlr is a long-read mapper designed to align PacBilo or Oxford Nanopore to a reference genome with a focus on reads that span structural variations

OrthoFinder

Phylogenetic orthology inference for comparative genomics

PASApipeline

PASA software

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

pilon

Ratatosk

Hybrid error correction of long reads using colored de Bruijn graphs

RepARK

Repetitive motif detection by Assembly of Repetitive K-mers

sandtrout

Accessory scripts for the MAKER annotation pipeline

StainedGlass

Make colorful identity heatmaps of genomic sequence

Tailor

Tailor is a fast short read aligner like bowtie/BWA/SOAP2 but is designed specifically to discovering trimming and tailing events for small silencing RNAs.