BOL: Related items

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Abhimanyu Singh — Tue, 23 May 2017 05:28:56 -0500

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1344-7

Address of the bookmark: http://ufmg-simba.sourceforge.net/

GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads

Jit — Mon, 14 May 2018 05:25:48 -0500

This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this documentation, is distributed free of charge. If you use this program in a publication, please cite the following reference:
Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." bioRxiv (2017): 125534.

Address of the bookmark: https://github.com/Reedwarbler/GAPPadder

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/

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm

BioStar — Mon, 16 Mar 2020 10:09:26 -0500

Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version at https://arxiv.org/pdf/1902.04341.pdf

More at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa179/5804978?rss=1

Address of the bookmark: https://github.com/CMU-SAFARI/Apollo

Scaffolding of a bacterial genome using MinION nanopore sequencing

Rahul Agarwal — Tue, 07 Jul 2015 16:59:25 -0500

Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program.

Address of the bookmark: http://www.nature.com/srep/2015/150707/srep11996/full/srep11996.html

NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore

Jit — Wed, 25 Apr 2018 07:30:54 -0500

CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows ngmlr to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling ngmlr to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions).

Address of the bookmark: https://github.com/philres/ngmlr

Nanopore adaptor !

Jit — Mon, 03 Feb 2020 00:10:29 -0600

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

The known Nanopore adapters that Porechop looks for are defined

https://github.com/rrwick/Porechop/blob/master/porechop/adapters.py

They are:

Ligation kit adapters
Rapid kit adapters
PCR kit adapters
Barcodes
Native barcoding
Rapid barcoding

Address of the bookmark: https://github.com/rrwick/Porechop/blob/master/porechop/adapters.py

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

Circlator: automated circularization of genome assemblies using long sequencing reads

Poonam Mahapatra — Tue, 15 May 2018 09:42:32 -0500

A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0. PMID: 26714481.

Address of the bookmark: http://sanger-pathogens.github.io/circlator/

SimLoRD: A read simulator for third generation sequencing reads

Aaryan Lokwani — Wed, 22 Aug 2018 10:40:27 -0500

SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model.

Reads are simulated from both strands of a provided or randomly generated reference sequence.

The reference can be read from a FASTA file or randomly generated with a given GC content. It can consist of several chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorporated at a later stage.)
The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampling from a a text file with integers (RNA), or using a fixed length
Quality values and number of passes depend on fragment length.
Provided subread error probabilities are modified according to number of passes
Outputs reads in FASTQ format and alignments in SAM format

Address of the bookmark: https://bitbucket.org/genomeinformatics/simlord/