Projects in Awesome Lists tagged with pacbio

https://github.com/fritzsedlazeck/sniffles

Structural variation caller using third generation sequencing

bioconda bioinformatics nanopore ngm-lr pacbio structural-variation structural-variations

Last synced: 14 May 2025

https://github.com/chhylp123/hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

bioinformatics denovo-assembly genomics hifi-read pacbio

Last synced: 05 May 2025

https://github.com/ruanjue/wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

alignment assembly nanopore pacbio

Last synced: 04 Apr 2025

https://github.com/nextomics/nextdenovo

Fast and accurate de novo assembler for long reads

assembler genome-assembly long-reads oxford-nanopore pacbio

Last synced: 05 Apr 2025

https://github.com/philres/ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

alignment bioconda docker long-read mapper next-generation-sequencing oxford-nanopore pacbio structural-variations

Last synced: 14 Apr 2025

https://github.com/chanzuckerberg/shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

assembly de-novo dna long-read nanopore pacbio sequencing

Last synced: 05 May 2025

https://github.com/Genetalks/gtz

A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.

bam compress compression compression-rate fastq fastq-compression gene genomic-data-compression gtx nanopore pacbio sam

Last synced: 07 May 2025

https://github.com/sequana/sequana

Sequana: a set of Snakemake NGS pipelines

coverage de-novo ngs pacbio rna-seq sequanix snakemake taxonomy variant-calling

Last synced: 16 May 2025

https://github.com/mortazavilab/TALON

Technology agnostic long read analysis pipeline for transcriptomes

oxford-nanopore pacbio transcript-quantification transcriptome

Last synced: 06 May 2025

https://github.com/ruanjue/smartdenovo

Ultra-fast de novo assembler using long noisy reads

assembler pacbio

Last synced: 10 Apr 2025

https://github.com/parklab/xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

illumina linked-reads mobile-element-insertion nanopore pacbio transposable-elements

Last synced: 14 Mar 2025

https://github.com/anuradhawick/lrbinner

LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.

bioinformatics metagenomic-analysis metagenomics metagenomics-binning nanopore-sequencing pacbio python

Last synced: 07 May 2025

https://github.com/fmalmeida/ngs-preprocess

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

bax2bam bioinformatics illumina nanopack nextflow ngs ngs-preprocess pacbio pacbio-ccs pipeline porechop reproducible-research reproducible-science trimgalore workflow

Last synced: 05 May 2025

https://github.com/vtsyvina/CliqueSNV

haplotypes illumina ngs pacbio quasispecies

Last synced: 23 Mar 2025

https://github.com/vmikk/nextits

A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio

eukaryotes fungi internal-transcribed-spacer its metabarcoding nextflow pacbio pipeline

Last synced: 10 Apr 2025

https://github.com/bioinformatist/py3_scripts

Life is short, *****.

blast crawler gtf pacbio scrapy

Last synced: 24 Apr 2025

https://github.com/nschan/nf-genomeassembly

Nextflow pipeline to assemble genomes from long reads.

annotation arabidopsis arabidopsis-thaliana genome genome-assembly genome-sequencing hifi long-read-sequencing long-reads nanopore nextflow nextflow-pipeline nextflow-pipelines oxford-nanopore pacbio pacbio-hifi-sequencing-reads scaffolding

Last synced: 17 Feb 2025

https://github.com/gauravcodepro/pacbio-nanopore-repeat-coverage

a long read repeat coverage calculator,given an long read file before assembly either direct from the sequencing runs or after the cleaning, it calculates the total amount of the repeat stretches present in the sequencing reads and you can plot them before assembly

bioinformatics bioinformatics-algorithms bioinformatics-tool longread oxford-nanopore pacbio pacbio-sequencing sequencing-coverage sequencing-data sequencing-error