<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38061?offset=20 https://bioinformaticsonline.com/bookmarks/view/26909/sequence-assembly-with-mira-4 Wed, 06 Apr 2016 08:21:22 -0500 https://bioinformaticsonline.com/bookmarks/view/26909/sequence-assembly-with-mira-4 <![CDATA[Sequence assembly with MIRA 4]]> MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by

  • electrophoresis sequencing (aka Sanger sequencing)

  • 454 pyro-sequencing (GS20, FLX or Titanium)

  • Ion Torrent

  • Solexa (Illumina) sequencing

  • (in development) Pacific Biosciences sequencing

into contiguous sequences (called contigs). One can use the sequences of different sequencing technologies either in a single assembly run (a true hybrid assembly) or by mapping one type of data to an assembly of other sequencing type (a semi-hybrid assembly (or mapping)) or by mapping a data against consensus sequences of other assemblies (a simple mapping).

The MIRA acronym stands for Mimicking Intelligent Read Assembly and the program pretty well does what its acronym says (well, most of the time anyway). It is the Swiss army knife of sequence assembly that I've used and developed during the past 14 years to get assembly jobs I work on done efficiently - and especially accurately. That is, without me actually putting too much manual work into it.

More at http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

Address of the bookmark: http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

]]> Priya Singh https://bioinformaticsonline.com/bookmarks/view/32129/lordec-a-hybrid-error-correction-program-for-long-pacbio-reads Mon, 10 Apr 2017 04:16:09 -0500 https://bioinformaticsonline.com/bookmarks/view/32129/lordec-a-hybrid-error-correction-program-for-long-pacbio-reads <![CDATA[LoRDEC: a hybrid error correction program for long, PacBio reads]]> LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and the PacBio read set, which is then corrected using the reference set. Typically, the reference set contains Illumina reads.


Usually, errors in PacBio reads include many insertions and deletions, and comparatively less substitutions. LoRDEC can correct errors of all these types.
After correction, a larger portion of the sequence of PacBio reads is usable for detection of region of similarity with other sequences, for aligning them to the contigs of an assembly, etc.

Why is LoRDEC different?

  • It is efficient and can process large read data sets, included from eukaryotic or vertebrate species, on a usual computing server, and even works on desktop/laptop computers.
  • It adopts a novel graph based approach: it builds a succinct De Bruijn Graph (DBG) representing the short reads, and seeks a corrective sequence for each erroneous region of a long read by traversing chosen paths in the graph.

Address of the bookmark: http://www.atgc-montpellier.fr/lordec/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37759/pandaseq-is-a-program-to-align-illumina-reads-optionally-with-pcr-primers-embedded-in-the-sequence-and-reconstruct-an-overlapping-sequence Fri, 21 Sep 2018 10:19:52 -0500 https://bioinformaticsonline.com/bookmarks/view/37759/pandaseq-is-a-program-to-align-illumina-reads-optionally-with-pcr-primers-embedded-in-the-sequence-and-reconstruct-an-overlapping-sequence <![CDATA[PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.]]> Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via:

sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config

On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must be installed, then:

sudo fink install bzip2-dev pkgconfig

Address of the bookmark: https://github.com/neufeld/pandaseq

]]> BioStar 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/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