<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38563?offset=30 https://bioinformaticsonline.com/bookmarks/view/40893/quorum-an-error-corrector-for-illumina-reads Tue, 04 Feb 2020 23:26:55 -0600 https://bioinformaticsonline.com/bookmarks/view/40893/quorum-an-error-corrector-for-illumina-reads <![CDATA[QuorUM: An Error Corrector for Illumina Reads]]> We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is efficiently implemented making use of current multi-core computing architectures and it is suitable for large data sets (1 billion bases checked and corrected per day per core)

Address of the bookmark: http://www.genome.umd.edu/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/34618/mashmap-a-fast-and-approximate-software-for-mapping-long-reads-pacbioont-or-assembly-to-reference-genomes Tue, 12 Dec 2017 17:23:31 -0600 https://bioinformaticsonline.com/bookmarks/view/34618/mashmap-a-fast-and-approximate-software-for-mapping-long-reads-pacbioont-or-assembly-to-reference-genomes <![CDATA[MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)]]> MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but rather estimates a k-mer based Jaccard similarity using a combination of Winnowing and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is automatically determined given minimum local alignment length and identity thresholds. The efficiency of the algorithm improves as both of these thresholds are increased.

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

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37737/rebaler-program-for-conducting-reference-based-assemblies-using-long-reads Tue, 18 Sep 2018 07:52:41 -0500 https://bioinformaticsonline.com/bookmarks/view/37737/rebaler-program-for-conducting-reference-based-assemblies-using-long-reads <![CDATA[Rebaler: program for conducting reference-based assemblies using long reads.]]> Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences.

I made Rebaler for bacterial genomes (specifically for the task of testing basecallers). It should in principle work for non-bacterial genomes as well, but I haven't tested it.

Address of the bookmark: https://github.com/rrwick/Rebaler

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41501/hicanu-accurate-assembly-of-segmental-duplications-satellites-and-allelic-variants-from-high-fidelity-long-reads Fri, 27 Mar 2020 22:49:31 -0500 https://bioinformaticsonline.com/bookmarks/view/41501/hicanu-accurate-assembly-of-segmental-duplications-satellites-and-allelic-variants-from-high-fidelity-long-reads <![CDATA[HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads]]> 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

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/31568/pacbio-long-reads-compatible-software-and-tools Wed, 15 Mar 2017 14:19:01 -0500 https://bioinformaticsonline.com/bookmarks/view/31568/pacbio-long-reads-compatible-software-and-tools <![CDATA[Pacbio Long Reads Compatible Software and Tools]]> 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

]]> Archana Malhotra https://bioinformaticsonline.com/bookmarks/view/35061/proovread-large-scale-high-accuracy-pacbio-correction-through-iterative-short-read-consensus Fri, 05 Jan 2018 04:12:20 -0600 https://bioinformaticsonline.com/bookmarks/view/35061/proovread-large-scale-high-accuracy-pacbio-correction-through-iterative-short-read-consensus <![CDATA[proovread : large-scale high-accuracy PacBio correction through iterative short read consensus]]> proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

proovread maps high coverage data to pacbio reads (bwa mem, blasr, daligner) in multiple iterations.

Address of the bookmark: https://github.com/BioInf-Wuerzburg/proovread

]]> 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/bookmarks/view/38735/genome-assembly-tutorial-genome-assembly-for-short-and-long-reads Sat, 19 Jan 2019 17:29:53 -0600 https://bioinformaticsonline.com/bookmarks/view/38735/genome-assembly-tutorial-genome-assembly-for-short-and-long-reads <![CDATA[Genome assembly tutorial "Genome Assembly for short and long reads"]]> In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will know:

  1. How to perform basic quality checks on the input data
  2. How to run a short read assembler on Illumina data
  3. How to run a long read assembler on Pacific Biosciences or Oxford Nanopore data
  4. How to improve the accuracy of a long read assembly using short reads
  5. How to assess the quality of an assembly

https://bioinformaticsdotca.github.io/high-throughput_biology_2017

Address of the bookmark: https://bioinformaticsdotca.github.io/high-throughput_biology_2017_module6_lab

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42946/aligngraph2-similar-genome-assisted-reassembly-pipeline-for-pacbio-long-reads Sun, 14 Mar 2021 09:42:47 -0500 https://bioinformaticsonline.com/bookmarks/view/42946/aligngraph2-similar-genome-assisted-reassembly-pipeline-for-pacbio-long-reads <![CDATA[AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads]]> AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.

More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/6146772

Address of the bookmark: https://github.com/huangs001/AlignGraph2

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/32868/pollux-platform-independent-error-correction-of-single-and-mixed-genomes Fri, 19 May 2017 09:41:27 -0500 https://bioinformaticsonline.com/bookmarks/view/32868/pollux-platform-independent-error-correction-of-single-and-mixed-genomes <![CDATA[Pollux: platform independent error correction of single and mixed genomes]]> Pollux: General-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0435-6

Address of the bookmark: https://github.com/emarinier/pollux

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