sanvva

ALLHiC

A package to scaffolding polyploidy or heterozygosis genome using Hi-C data

OM-HiC-scaffolding

Workflows for correcting and scaffolding long-read (PacBio, nanopore) genome assemblies using optical mapping and/or Dovetail Hi-C data

assembly-stats

Get assembly statistics from FASTA and FASTQ files

blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

BTSearcher

BTSearcher for mac.

Chloroplast-genome-single-copy-orientation-ratio-detection

Estimate the ratio of different directions of single copy in the chloroplast genome

Chroloplast-genome-assembly

A pipeline for assemble chroloplast genome using short/long reads

Comparative-Annotation-Toolkit

editTools

:mag_right: Detection and analysis of RNA editing evidence from VCF data

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)

Fastq_clean

Fastq_clean is optimised to batchly clean the NGS data from the IlluminaTM sequencer

Flye

Fast and accurate de novo assembler for single molecule sequencing reads

gawn

GAWN - Genome Annotation Without Nightmares

Genome-data-of-Hanfu-apple

FASTA files of chromosomes and genes, gff files for gene models.

GenomeAlign

hello-world

just begin

LTR_retriever

A highly accurate and sensitive program to identify LTR retrotransposons

medusa

A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

pbalign

pbalign maps PacBio reads to reference sequences and saves alignments to a BAM file

PGA

Plastid Genome Annotation

pipeline-for-isoseq

quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

shovill

Faster SPAdes assembly of Illumina reads

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

Unicycler

hybrid assembly pipeline for bacterial genomes

wgd

Python package and CLI for whole genome duplication analyses

wtdbg-1.2.8

Important update of wtdbg