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acc2tax

Tool for quick offline batch conversion of Genbank IDs or accessions to taxonomy strings

adaptorfinder

tools that finds adaptor unremoved subreads

aligngraph

Algorithm for secondary de novo genome assembly guided by closely related references

annot-nf

Eukaryotic genome annotation pipeline implemented in Nextflow

apm_planner

APM Planner Ground Control Station (Qt)

apps-scripts

Miscellaneous scripts for applications of PacBio systems

arkshellgenome

Scripts used in chromosome-level genome assembly of ark shell

assembly-stats

Get assembly statistics from FASTA and FASTQ files

assembly_improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

assemblystatistics

A simple program for evaluate the assembly of a give genome.

assemblyutility

axidraw

Software for the AxiDraw drawing machine

barcodeanalysis

A python library of tools and prototypes for analyzing barcoded PacBio barcode data

barcoding

Lima - Demultiplex Barcoded PacBio Samples

basemod-3.0

berokka

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

biflow

bio_assembly_refinement

Tools to refine/finish an assembly

bioinformatics-training

Bioinformatics training resources

bioinformatics-workbook

bionanoanalyst

BioNanoAnalyst is a tool providing GUI to assess the genome assembly quality using BioNano data.

bioutil

A collection of bioinformatic scripts

busco-mod

Modified Version of BUSCO (http://busco.ezlab.org)

c3s-laa

Clustering of Circular Consensus Sequences (C3S) for Long Amplicon Analysis of PacBio Data

canu

A single molecule sequence assembler for genomes large and small.

cdna_primer

Scripts for processing PacBio transcriptome (Iso-Seq) data

cegma_v2

The final version 2 release of our software to detect core genes in eukaryotic genomes

chatcode

Bioinformatics scripts generated by openai ChatGPT

chrvis

a chromosome visualization tool

circlator

A tool to circularize genome assemblies