BOL: Related items

mScaffolder: A comparative genome scaffolding tool

Jit — Fri, 15 Jun 2018 04:48:01 -0500

A comparative genome scaffolding tool based on MUMmer

mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guided by their alignments to the reference genome. Please send your questions and comments to mchakrab@uci.edu.

Citation https://www.nature.com/articles/s41588-017-0010-y

Address of the bookmark: https://github.com/mahulchak/mscaffolder

GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments

Shruti Paniwala — Mon, 11 Jun 2018 05:43:44 -0500

GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap closure. We demonstrate with sequencing data from various organisms that the gap-closing accuracy of GMcloser is 3–100-fold higher than those of other available tools, with similar efficiency. https://academic.oup.com/bioinformatics/article/31/23/3733/209212

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/23/3733/209212

Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies

Jit — Sat, 31 Aug 2019 11:30:41 -0500

Chromosome-level genome assembler combining multiple de novo assemblies

https://github.com/jkimlab/IMAP

Address of the bookmark: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0221858

SVbyEye: R Package to visualize alignments between two or multiple DNA sequences

LEGE — Tue, 17 Sep 2024 02:34:57 -0500

R Package to visualize alignments between two or multiple DNA sequences including
a number of functionalities to facilitate processing of alignments in PAF format.

SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence alignments along with various functionalities to process alignments in PAF format. The tool facilitates the characterization of complex SVs in the context of sequence homology helping resolve the mechanisms underlying their formation. Availability and implementation SVbyEye is available at https://github.com/daewoooo/SVbyEye.

Author: David Porubsky

Address of the bookmark: https://github.com/daewoooo/SVbyEye

Software for genome assembly !

LEGE — Sun, 30 Aug 2020 09:51:38 -0500

List of bioinformatics tools/Software Website References for genome assembly:

1 Falcon https://github.com/PacificBiosciences/pb-assembly

2 Canu assembler http://canu.readthedocs.io/en/latest/index.html

3 Miniasm assembler https://github.com/lh3/miniasm

4 PBJelly scaffolding tool https://sourceforge.net/projects/pb-jelly/

5 ARCS scaffolding tool https://github.com/bcgsc/arcs

6 Redundans reduction and scaffolding tool https://github.com/Gabaldonlab/redundans

7 Arrow error correction https://github.com/PacificBiosciences/ GenomicConsensus

8 PILON error correction https://github.com/broadinstitute/pilon/wiki

9 BUSCO single copy gene markers http://busco.ezlab.org/

10 Bandage graph assembly viewer https://rrwick.github.io/Bandage/

11 Gepard dotter http://cube.univie.ac.at/gepard

12 MUMmer aligner and plotter http://mummer.sourceforge.net/

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

SWALO: Scaffolding with assembly likelihood optimization

Jit — Wed, 20 Jun 2018 02:45:16 -0500

SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.

Address of the bookmark: https://atifrahman.github.io/SWALO/

ARCS: scaffolding genome drafts with linked reads

Rahul Nayak — Tue, 06 Mar 2018 16:35:26 -0600

ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data for connecting high-quality sequences in genome assembly drafts.

Address of the bookmark: https://github.com/bcgsc/ARCS/

ARCS: scaffolding genome drafts with linked reads

Jit — Mon, 17 Dec 2018 17:40:28 -0600

ARCS requires two input files:

Draft assembly fasta file
Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)

Address of the bookmark: https://github.com/bcgsc/ARCS/

HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

Jit — Sat, 08 May 2021 21:25:00 -0500

HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies.

Address of the bookmark: https://github.com/esolares/HapSolo