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actc

Align subreads to ccs reads

angel

Robust Open Reading Frame prediction (ANGLE re-implementation)

apps-scripts

Miscellaneous scripts for applications of PacBio systems

bam2fastx

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

barcoding

Lima - Demultiplex Barcoded PacBio Samples

c3s

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

ccs

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

cosa

SARS-CoV-2 analysis using PacBio long reads

daligner

Find all significant local alignments between reads

damapper

Long read to reference genome mapping tool

damasker

Module to determine where repeats are and make soft-masks of said

dazz_db

The Dazzler Data Base

devnet

The DevNet project on github stores the PacBio DevNet website.

dextractor

Bax File Decoder and Data Compressor

extracthifi

Extract PacBio HiFi reads from CCS BAM files

falcon

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

falcon-integrate

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

falcon-pbsmrtpipe

run.py etc using pbsmrtpipe instead of pypeFLOW

falcon-polish

Workflow which runs FALCON followed by polishing.

falcon3

falcon in python3

falcon_unzip

Making diploid assembly becomes common practice for genomic study

falcon_unzip3

falcon-unzip in python3

gcpp

hg002-ccs

hifi-16s-workflow

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

hifi-amplicon-workflow

HiFi Amplicon Workflow

hifi-human-assembly-wdl

hifi-human-wgs-wdl

hifi-mag-wdl

WDL workflow for metagenomics