BOL: Related items

RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes

Rahul Nayak — Fri, 01 May 2020 03:00:40 -0500

RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.

Address of the bookmark: https://github.com/AppliedBioinformatics/RefKA

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Abhi — Wed, 06 Oct 2021 07:01:14 -0500

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

UniAligner: a parameter-free framework for fast sequence alignment

Abhi — Fri, 08 Mar 2024 23:36:12 -0600

UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches, such as the Smith-Waterman algorithm, that work well for most sequences, fail to construct biologically adequate alignments of extra-long tandem repeats (ETRs), such as human centromeres and immunoglobulin loci. This limitation was overlooked in the previous studies since the sequences of the centromeres and other ETRs across multiple genomes only became available recently.

More at https://www.nature.com/articles/s41592-023-01970-4

Address of the bookmark: https://github.com/seryrzu/unialigner

Termal: a fast and interactive terminal-based viewer for multiple sequence alignments

LEGE — Mon, 22 Sep 2025 23:51:02 -0500

termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC) clusters.

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads

Jit — Mon, 27 Feb 2017 09:49:45 -0600

FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.

Address of the bookmark: http://kakitone.github.io/finishingTool/

npScarf: Scaffolding and Completing Assemblies in Real-time Fashion

Jit — Tue, 23 May 2017 04:53:29 -0500

npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It also facilitates the real-time analysis of positional information such as gene ordering and the detection of genes from mobile elements (plasmids and genomic islands).

Complete paper at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321748/

Address of the bookmark: https://github.com/mdcao/npScarf

The MARVEL assembler

Jit — Fri, 04 May 2018 19:18:41 -0500

MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.

The assembly process can be summarized as follows:

overlap
patch reads
overlap (again)
scrubbing
assembly graph construction and touring
optional read correction
fasta file creation

Address of the bookmark: https://github.com/schloi/MARVEL

Phased Human Genome Assembly !

Rahul Nayak — Mon, 08 Oct 2018 09:10:54 -0500

The new publicly available assembly (PacBio HG00733) has the fewest gaps of any human genome assembly, with more than half of the genome contained in gapless sequence at least 27 Mb long. The primary contig assembly is 2.89 Gb long and consists of 865 contigs that were assembled with PacBio data generated with the company’s Sequel® System. Using the FALCON-Unzip assembler, maternal and paternal haplotypes were resolved over more than 80% of the genome. Maternal and paternal haplotype blocks were then further phased using Hi-C technology and the FALCON-Phase methoddeveloped in collaboration with Phase Genomics. The genome was then de novo scaffolded using Phase Genomics’ Proximo Hi-C platform, resulting in the first chromosome-scale diploid assembly of a single individual accomplished with only two technologies. More specific details about the assembly are included on the PacBio blog.

The data are available using NCBI accession IDs: BioProject: (PRJNA483067), assembly: [RBJD00000000] and sequence data (SRP155659).

Additional Resources

Interactive map showcasing global initiatives underway to generate reference-quality human genome assemblies for diverse populations
BioReport Podcast on the value of ethnic-specific reference genomes
Nature Reviews Genetics paper from NHGRI: Prioritizing diversity in human genomics research
Article in The Journal of Precision Medicine: “Minority Report – Ethnic Diversity and the Real Promise for Precision Medicine”
Article in Bio-IT World: “Genomic Data Standards Are a Necessity”
NHGRI Project Award: High Quality Human and Non-Human Primate Genome Assemblies

More details are available on the PacBio website:

Blog post: Data Release: Highest-Quality, Most Contiguous Individual Human Genome Assembly to Date
Blog post: For Reference-Grade Human Genome Assemblies, SMRT Sequencing Yields Optimal Results
Webinar: Assembling High-Quality Human Reference Genomes for Global Populations
FALCON-Phase press release and article preprint
PacBio research focus webpage about Human Population Genetics

Ref: https://stockguru.com/2018/10/08/pacific-biosciences-releases-highest-quality-most-contiguous-individual-human-genome-assembly-to-date/

pbmm2:A minimap2 frontend for PacBio native data formats

BioStar — Tue, 18 Feb 2020 03:36:22 -0600

pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.

Address of the bookmark: https://github.com/PacificBiosciences/pbmm2

Pacbio Long Reads Compatible Software and Tools

Archana Malhotra — Wed, 15 Mar 2017 14:19:01 -0500

The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual project sites for up-to-date license information. A separate page lists commercial software.

Know of any other open source software for PacBio data? Email us.

Software categories:

Address of the bookmark: https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software