<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38505?offset=210 https://bioinformaticsonline.com/bookmarks/view/37785/haplomerger2-rebuilding-both-haploid-sub-assemblies-from-high-heterozygosity-diploid-genome-assembly Thu, 27 Sep 2018 07:08:47 -0500 https://bioinformaticsonline.com/bookmarks/view/37785/haplomerger2-rebuilding-both-haploid-sub-assemblies-from-high-heterozygosity-diploid-genome-assembly <![CDATA[HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly]]> HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliable gap-closing method for haploid sub-assemblies.

Source code, executables and the testing dataset are freely available at https://github.com/mapleforest/HaploMerger2/releases/.

Address of the bookmark: https://github.com/mapleforest/HaploMerger2/releases/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/38063/referee-genome-assembly-quality-scores Sun, 04 Nov 2018 16:44:30 -0600 https://bioinformaticsonline.com/bookmarks/view/38063/referee-genome-assembly-quality-scores <![CDATA[Referee: Genome assembly quality scores]]> Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site in an assembled genome to calculate a quality score for each position in the genome assembly.

We accomplish this by first calculating genotype likelihoods for every site. For a given site in a diploid genome, there are 10 possible genotypes (AA, AC, AG, AT, CC, CG, CT, GG, GT, TT). Referee takes as input the genotype likelihoods calculated for all 10 genotypes given the called reference base at each position.

Referee is a program to calculate a quality score for every position in a genome assembly. This allows for easy filtering of low quality sites for any downstream analysis.

https://github.com/gwct/referee

Address of the bookmark: https://gwct.github.io/referee/#

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38526/versatile-genome-assembly-evaluation-with-quast-lg Fri, 21 Dec 2018 22:06:31 -0600 https://bioinformaticsonline.com/bookmarks/view/38526/versatile-genome-assembly-evaluation-with-quast-lg <![CDATA[Versatile genome assembly evaluation with QUAST-LG]]> QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size).

QUAST-LG is included in the QUAST  package starting from version 5.0.0 (download the latest release). Run QUAST as usual and do not forget to add ‐‐large option to your command!

A short list of the new features (see CHANGES for all):

  • Significant speedup achieved by both use of new fast aligner (minimap2) and the refactoring of alignment analyzing modules
  • New k-mer-based completeness and correctness metrics
  • BUSCO added for enhanced reference-free analysis
  • The concept of upper bound assembly (theoretical limits on the assembly completeness and contiguity for a given genome and set of reads)

Address of the bookmark: http://cab.spbu.ru/software/quast-lg/

]]> Jit https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly Tue, 22 Jan 2019 09:39:02 -0600 https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly <![CDATA[List of tools frequently used while genome assembly]]> List of tools frequently used while genome assembly:

I have used the following assemblers

I have used the following mappers

I have used the following polishing tools

I have used the following tools to assess genome assembly characteristics

If you have any ideas or superior tools we have missed please let us know in the comments.

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/38892/wtdbg2-a-fuzzy-bruijn-graph-approach-to-long-noisy-reads-assembly Mon, 04 Feb 2019 04:53:47 -0600 https://bioinformaticsonline.com/bookmarks/view/38892/wtdbg2-a-fuzzy-bruijn-graph-approach-to-long-noisy-reads-assembly <![CDATA[wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly]]> Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. 

./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix
./wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa

Address of the bookmark: https://github.com/ruanjue/wtdbg2

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/40598/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization Fri, 24 Jan 2020 04:09:15 -0600 https://bioinformaticsonline.com/bookmarks/view/40598/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization <![CDATA[MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization]]> MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization. MitoZ is available from https://github.com/linzhi2013/MitoZ.

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics Tue, 17 Mar 2020 06:19:06 -0500 https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics <![CDATA[JCVI:Python utility libraries on genome assembly, annotation and comparative genomics]]> Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

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

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41599/haslr-a-hybrid-assembler-which-uses-both-second-and-third-generation-sequencing-reads Mon, 04 May 2020 02:04:03 -0500 https://bioinformaticsonline.com/bookmarks/view/41599/haslr-a-hybrid-assembler-which-uses-both-second-and-third-generation-sequencing-reads <![CDATA[HASLR: a hybrid assembler which uses both second and third generation sequencing reads]]> HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.

Address of the bookmark: https://github.com/vpc-ccg/haslr

]]> BioStar https://bioinformaticsonline.com/blog/view/42166/software-for-genome-assembly Sun, 30 Aug 2020 09:51:38 -0500 https://bioinformaticsonline.com/blog/view/42166/software-for-genome-assembly <![CDATA[Software for genome assembly !]]> 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/

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/43614/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization Tue, 30 Nov 2021 23:23:57 -0600 https://bioinformaticsonline.com/bookmarks/view/43614/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization <![CDATA[MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization]]> MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads.

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

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