Discover PacificBiosciences/XiSkewAnalysis Open Source project

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

204

pbbioconda

202

pbmm2

A minimap2 frontend for PacBio native data formats

Perl

162

IsoSeq

IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

149

pb-metagenomics-tools

Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics

HTML

132

pb-assembly

PacBio Assembly Tool Suite: Reads in ⇨ Assembly out

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

110

ccs

108

pbsv

pbsv - PacBio structural variant (SV) calling and analysis tools

Tandem repeat genotyping and visualization from PacBio HiFi data

trgt

Rust

barcoding

Lima - Demultiplex Barcoded PacBio Samples

HiFi-16S-workflow

Nextflow pipeline to analyze PacBio HiFi full-length 16S data

Nextflow

HiFi-human-WGS-WDL

Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads

HiPhase

Rust

sv-benchmark

Public Benchmark of Long-Read Structural Variant Caller on PacBio CCS HG002 Data

pb-CpG-tools

Collection of tools for the analysis of CpG data

primrose

Predict 5mC in PacBio HiFi reads

pbcore

A Python library for reading and writing PacBio® data files

Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files.

bam2fastx

svpack

Structural variant (SV) analysis tools

Mostly deprecated. See https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

FALCON-integrate

Shell

FALCON_unzip

Making diploid assembly becomes common practice for genomic study

Copy number variant caller and depth visualization utility for PacBio HiFi reads

HiFiCNV

Shell

PacBioFileFormats

Specifications for PacBio® native file formats

Improved Phased Assembler

pbtk

PacBio BAM toolkit

pbipa

apps-scripts

Miscellaneous scripts for applications of PacBio systems

pbbam

PacBio BAM C++ library

An HLA star-calling tool for PacBio HiFi data types

pbAA

hifihla

pbfusion

Tools for detecting DNA modifications from single molecule, real-time sequencing data

kineticsTools

Robust Open Reading Frame prediction (ANGLE re-implementation)

ANGEL

Minor Variant Calling and Phasing Tools

minorseq

hg002-ccs

A battery of methylation tools for PacBio HiFi reads

MethBat

paraphase

HiFi-based caller for highly homologous genes

Align subreads to ccs reads

actc

pb-human-wgs-workflow-wdl

pancake

a simple lightweight workflow engine for data analysis scripting

pypeFLOW

HTML

HiFiTargetEnrichment

A repo for the Twist HiFi capture/snakemake workflow

pangu

Tumor-normal variant calling workflow using HiFi reads

HiFi-somatic-WDL

exploratory scripts for clustering ccs amplicon data

pbampliconclustering

PacBio common models, CLI tool contract interface and SMRT Link Service Interface

pbcommand

TRGT Repeat expansion summary

gcpp

TRexs

jasmine

Predict 5mC in PacBio HiFi reads

pb-StarPhase

A phase-aware pharmacogenomic diplotyper for PacBio datasets

trgt-denovo

De novo tandem repeat calling from PacBio HiFi data

Rust

pbcopper

Core C++ library for data structures, algorithms, and utilities

HiFi-human-assembly-WDL

SARS-CoV-2 analysis using PacBio long reads

CoSA

wdl-common

Mark duplicate reads from PacBio sequencing of an amplified library

pbmarkdup

hifi-amplicon-workflow

HiFi Amplicon Workflow

SKERA - Deconcat PacBio reads

skera

harmony

Compute error profiles from alignments

wdl-dockerfiles

Generates one consensus sequence of all input CCS reads, using partial order alignment

c3s

Extract PacBio HiFi reads from CCS BAM files

extracthifi

FALCON-polish

Workflow which runs FALCON followed by polishing.

A tool to recall adapters for PacBio data

recalladapters

reference_genomes

Shell

pigeon

HiFi-MAG-WDL

WDL workflow for metagenomics

Small datasets for testing

PacBioTestData

The project to host release binary LAA/LAAgc on bioconda

zmwfilter

Filter PacBio BAM files

pblaa

FALCON-pbsmrtpipe

run.py etc using pbsmrtpipe instead of pypeFLOW