BOL: Related items

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

BioStar — Fri, 27 Mar 2020 22:49:31 -0500

HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering.

More at https://www.biorxiv.org/content/10.1101/2020.03.14.992248v3

Address of the bookmark: https://github.com/marbl/canu

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Jit — Thu, 24 Dec 2020 10:03:36 -0600

Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce primary/alternate assemblies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data.

Address of the bookmark: https://github.com/chhylp123/hifiasm

dna2bit: an ultra-fast and accurate genomic distance estimation software

LEGE — Sun, 31 Aug 2025 06:24:58 -0500

dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and MacOS platforms.

Address of the bookmark: https://github.com/lijuzeng/dna2bit

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

Genome Browsers

Rahul Agarwal — Fri, 16 Aug 2013 19:04:47 -0500

Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.

Following are the weblink for different available browsers:

http://www.ensembl.org/index.html

http://ensemblgenomes.org/

http://genome.ucsc.edu/

http://www.ncbi.nlm.nih.gov/genome

http://www.ebi.ac.uk/genomes/

http://flybase.org/

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://www.sanger.ac.uk/resources/databases/

NCBI Remap

Jit — Thu, 11 Feb 2016 11:02:26 -0600

NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use the API for NCBI Remap.

More at http://www.ncbi.nlm.nih.gov/genome/tools/remap

API http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api

Address of the bookmark: http://www.ncbi.nlm.nih.gov/genome/tools/remap

AnnotationSketch

Jit — Sun, 25 Jun 2017 17:54:22 -0500

The AnnotationSketch module is a versatile and efficient C-based drawing library for GFF3-compatible genomic annotations. It is included in the GenomeTools distribution. Additionally, bindings to the Lua, Python and Rubyprogramming languages are provided.

http://genometools.org/annotationsketch.html

Address of the bookmark: http://genometools.org/annotationsketch.html

MFannot : a program for the annotation of mitochondrial and plastid genomes

Jit — Mon, 26 Aug 2019 11:47:56 -0500

MFannot is a program for the annotation of mitochondrial and plastid genomes

MFannot is a program for the annotation of mitochondrial and plastid genomes. It is a PERL wrapper around a set of diverse, external independent tools.

It makes intense use of RNA/intron detection tools including HMMER, Exonerate, Erpin and others.

http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl

Address of the bookmark: https://github.com/BFL-lab/Mfannot

NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences

Jit — Tue, 05 May 2020 10:35:48 -0500

NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences. These features make NucDiff to be perfectly suitable to compare assemblies with each other or with available reference genomes.

NucDiff provides information about the types of differences and their locations. It is possible to upload the results into genome browser for visualization and further inspection. It was written in Python and uses the NUCmer package from MUMmer[1] for sequence comparison.

Address of the bookmark: https://github.com/uio-cels/NucDiff

JCVI utility libraries

Jit — Sat, 08 May 2021 22:04:02 -0500

Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Address of the bookmark: https://github.com/tanghaibao/jcvi