<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/32943?offset=10 https://bioinformaticsonline.com/bookmarks/view/40814/accesssyri-finding-genomic-rearrangements-and-local-sequence-differences-from-whole-genome-assemblies Sat, 01 Feb 2020 13:38:49 -0600 https://bioinformaticsonline.com/bookmarks/view/40814/accesssyri-finding-genomic-rearrangements-and-local-sequence-differences-from-whole-genome-assemblies <![CDATA[AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies]]> AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies

SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0

Address of the bookmark: https://github.com/schneebergerlab/syri

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36895/npscarf-real-time-scaffolder-using-spades-contigs-and-nanopore-sequencing-reads Mon, 11 Jun 2018 05:14:57 -0500 https://bioinformaticsonline.com/bookmarks/view/36895/npscarf-real-time-scaffolder-using-spades-contigs-and-nanopore-sequencing-reads <![CDATA[npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads]]> Address of the bookmark: http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html

]]> Shruti Paniwala 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/36403/ngmlr-long-read-mapper-designed-to-align-pacbio-or-oxford-nanopore Wed, 25 Apr 2018 07:30:54 -0500 https://bioinformaticsonline.com/bookmarks/view/36403/ngmlr-long-read-mapper-designed-to-align-pacbio-or-oxford-nanopore <![CDATA[NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore]]> CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows ngmlr to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling ngmlr to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions).

Address of the bookmark: https://github.com/philres/ngmlr

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36758/pbalign-maps-pacbio-reads-to-reference-sequences-and-saves-alignments-to-a-bam-file Thu, 24 May 2018 10:06:52 -0500 https://bioinformaticsonline.com/bookmarks/view/36758/pbalign-maps-pacbio-reads-to-reference-sequences-and-saves-alignments-to-a-bam-file <![CDATA[pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file]]> Address of the bookmark: https://github.com/PacificBiosciences/pbalign

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment Thu, 06 Sep 2018 16:27:35 -0500 https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment <![CDATA[LSC: Improving PacBio Long Read Accuracy by Short Read Alignment]]>
  • Added Command line argument support.
  • Multi-stage execution modes.
  • Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N.
  • Better compressed intermediate files.
  • Added utilities folder.
  • Added support for multiple short read files.
  • Removed use of configuration file.

    • Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/bookmarks/view/39640/flas-fast-and-high-throughput-algorithm-for-pacbio-long-read-self-correction Sat, 22 Jun 2019 12:16:39 -0500 https://bioinformaticsonline.com/bookmarks/view/39640/flas-fast-and-high-throughput-algorithm-for-pacbio-long-read-self-correction <![CDATA[FLAS: fast and high throughput algorithm for PacBio long read self-correction.]]> FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes misalignments for accuracy.

    Address of the bookmark: https://github.com/baoe/flas

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/43090/loretta-a-user-friendly-tool-for-assembling-viral-genomes-from-pacbio-sequence-data Wed, 23 Jun 2021 07:54:53 -0500 https://bioinformaticsonline.com/bookmarks/view/43090/loretta-a-user-friendly-tool-for-assembling-viral-genomes-from-pacbio-sequence-data <![CDATA[LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data]]> LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads.

    https://academic.oup.com/ve/article/7/1/veab042/6248116

    Address of the bookmark: https://academic.oup.com/ve/article/7/1/veab042/6248116

    ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2 Mon, 10 Apr 2017 04:45:40 -0500 https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2 <![CDATA[WGS Celera Assembler version 8.3rc2]]> These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.

    This distribution package provides a stable, tested, documented version of the software.  The distribution is usable on most Unix-like platforms, and some platforms have pre-compiled binary distributions ready for installation.

    The source code package includes full source code (revision 4627), Makefiles, and scripts.  A subset of the kmer package (http://kmer.sourceforge.net/, version r1994), used by some modules of Celera Assembler, is included.  This distribution includes [http://samtools.sourceforge.net/ SAMtools], [http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish 2.0], [https://github.com/pbjd/pbutgcns PBUTGCNS], [https://github.com/PacificBiosciences/pbdagcon PBDAGCON], [https://github.com/PacificBiosciences/BLASR BLASR], and parts of the [https://github.com/PacificBiosciences/FALCON/tree/v0.1.3 Falcon assembler].

    Full documentation can be found online at http://wgs-assembler.sourceforge.net/.

    Interesting scripts within it

    urbe@urbo214b[bin] ls                                                        []
    -rwxrwxr-x 1 urbe urbe  11K Apr 10 11:41 addCNSToStore
    -rwxrwxr-x 1 urbe urbe 575K Apr 10 11:41 addReadsToUnitigs
    -rwxrwxr-x 1 urbe urbe 128K Apr 10 11:41 analyzeBest
    -rwxrwxr-x 1 urbe urbe 257K Apr 10 11:41 analyzePosMap
    -rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 analyzeScaffolds
    -rwxrwxr-x 1 urbe urbe 224K Apr 10 11:41 asmOutputFasta
    -rwxrwxr-x 1 urbe urbe 448K Apr 10 11:41 asmOutputStatistics
    -rwxrwxr-x 1 urbe urbe 2,4K Apr 10 11:41 asmToAGP.pl
    -rwxrwxr-x 1 urbe urbe 7,6M Apr 10 11:41 blasr
    -rwxrwxr-x 1 urbe urbe 1,6M Apr 10 11:41 bogart
    -rwxrwxr-x 1 urbe urbe 183K Apr 10 11:41 bogus
    -rwxrwxr-x 1 urbe urbe 272K Apr 10 11:41 bogusness
    -rwxrwxr-x 1 urbe urbe 247K Apr 10 11:41 buildPosMap
    -rwxrwxr-x 1 urbe urbe 213K Apr 10 11:41 buildRefContigs
    -rwxrwxr-x 1 urbe urbe 990K Apr 10 11:41 buildUnitigs
    -rwxrwxr-x 1 urbe urbe  18K Apr 10 11:41 ca2ace.pl
    -rwxrwxr-x 1 urbe urbe  12K Apr 10 11:41 caqc_help.ini
    -rwxrwxr-x 1 urbe urbe  61K Apr 10 11:41 caqc.pl
    -rwxrwxr-x 1 urbe urbe  23K Apr 10 11:41 cat-corrects
    -rwxrwxr-x 1 urbe urbe  24K Apr 10 11:41 cat-erates
    -rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 cgw
    -rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 cgwDump
    -rwxrwxr-x 1 urbe urbe 204K Apr 10 11:41 chimChe
    -rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 chimera
    -rwxrwxr-x 1 urbe urbe 220K Apr 10 11:41 classifyMates
    -rwxrwxr-x 1 urbe urbe 201K Apr 10 11:41 classifyMatesApply
    -rwxrwxr-x 1 urbe urbe 215K Apr 10 11:41 classifyMatesPairwise
    -rwxrwxr-x 1 urbe urbe 366K Apr 10 11:41 computeCoverageStat
    -rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 convert-fasta-to-v2.pl
    -rwxrwxr-x 1 urbe urbe  48K Apr 10 11:41 convertOverlap
    -rwxrwxr-x 1 urbe urbe 119K Apr 10 11:41 convertSamToCA
    -rwxrwxr-x 1 urbe urbe  20K Apr 10 11:41 convertToPBCNS
    -rwxrwxr-x 1 urbe urbe 197K Apr 10 11:41 correct-frags
    -rwxrwxr-x 1 urbe urbe 259K Apr 10 11:41 correct-olaps
    -rwxrwxr-x 1 urbe urbe 520K Apr 10 11:41 correctPacBio
    -rwxrwxr-x 1 urbe urbe 540K Apr 10 11:41 ctgcns
    -rwxrwxr-x 1 urbe urbe 162K Apr 10 11:40 deduplicate
    -rwxrwxr-x 1 urbe urbe  37K Apr 10 11:41 demotePosMap
    -rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 dumpCloneMiddles
    -rwxrwxr-x 1 urbe urbe 124K Apr 10 11:41 dumpPBRLayoutStore
    -rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 dumpSingletons
    -rwxrwxr-x 1 urbe urbe 171K Apr 10 11:41 erate-estimate
    -rwxrwxr-x 1 urbe urbe 221K Apr 10 11:40 estimate-mer-threshold
    -rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 extendClearRanges
    -rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 extendClearRangesPartition
    -rwxrwxr-x 1 urbe urbe 205K Apr 10 11:40 extractmessages
    -rwxrwxr-x 1 urbe urbe 7,2M Apr 10 11:41 falcon_sense
    -rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 fastaToCA
    -rwxrwxr-x 1 urbe urbe 124K Apr 10 11:40 fastqAnalyze
    -rwxrwxr-x 1 urbe urbe 137K Apr 10 11:40 fastqSample
    -rwxrwxr-x 1 urbe urbe  62K Apr 10 11:40 fastqSimulate
    -rwxrwxr-x 1 urbe urbe 121K Apr 10 11:40 fastqSimulate-sort
    -rwxrwxr-x 1 urbe urbe 246K Apr 10 11:40 fastqToCA
    -rwxrwxr-x 1 urbe urbe 140K Apr 10 11:41 filterOverlap
    -rwxrwxr-x 1 urbe urbe 341K Apr 10 11:40 finalTrim
    -rwxrwxr-x 1 urbe urbe 228K Apr 10 11:41 fixUnitigs
    -rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 fragmentDepth
    -rwxrwxr-x 1 urbe urbe  29K Apr 10 11:41 fragsInVars
    -rwxrwxr-x 1 urbe urbe 545K Apr 10 11:41 frgs2clones
    -rwxrwxr-x 1 urbe urbe 398K Apr 10 11:40 gatekeeper
    -rwxrwxr-x 1 urbe urbe 139K Apr 10 11:40 gatekeeperbench
    -rwxrwxr-x 1 urbe urbe 167K Apr 10 11:40 gkpStoreCreate
    -rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 gkpStoreDumpFASTQ
    -rwxrwxr-x 1 urbe urbe 184K Apr 10 11:41 greedyFragmentTiling
    -rwxrwxr-x 1 urbe urbe 1,6K Apr 10 11:41 greedy_layout_to_IUM
    -rwxrwxr-x 1 urbe urbe 142K Apr 10 11:40 initialTrim
    -rwxrwxr-x 1 urbe urbe 967K Apr 10 11:41 jellyfish
    -rwxrwxr-x 1 urbe urbe 219K Apr 10 11:41 markRepeatUnique
    -rwxrwxr-x 1 urbe urbe 273K Apr 10 11:40 markUniqueUnique
    -rwxrwxr-x 1 urbe urbe 114K Apr 10 11:40 mercy
    -rwxrwxr-x 1 urbe urbe 3,8K Apr 10 11:41 mergeqc.pl
    -rwxrwxr-x 1 urbe urbe 422K Apr 10 11:40 merTrim
    -rwxrwxr-x 1 urbe urbe 125K Apr 10 11:40 merTrimApply
    -rwxrwxr-x 1 urbe urbe 376K Apr 10 11:40 meryl
    -rwxrwxr-x 1 urbe urbe 176K Apr 10 11:41 metagenomics_ovl_analyses
    -rwxrwxr-x 1 urbe urbe 297K Apr 10 11:41 olap-from-seeds
    -rwxrwxr-x 1 urbe urbe 275K Apr 10 11:41 outputLayout
    -rwxrwxr-x 1 urbe urbe 229K Apr 10 11:41 overlapInCore
    -rwxrwxr-x 1 urbe urbe 144K Apr 10 11:40 overlap_partition
    -rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStats
    -rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStore
    -rwxrwxr-x 1 urbe urbe 153K Apr 10 11:41 overlapStoreBucketizer
    -rwxrwxr-x 1 urbe urbe 175K Apr 10 11:41 overlapStoreBuild
    -rwxrwxr-x 1 urbe urbe  33K Apr 10 11:41 overlapStoreIndexer
    -rwxrwxr-x 1 urbe urbe  48K Apr 10 11:41 overlapStoreSorter
    -rwxrwxr-x 1 urbe urbe 604K Apr 10 11:40 overmerry
    lrwxrwxrwx 1 urbe urbe    4 Apr 10 11:41 pacBioToCA -> PBcR
    -rwxrwxr-x 1 urbe urbe 131K Apr 10 11:41 PBcR
    -rwxrwxr-x 1 urbe urbe 2,9M Apr 10 11:41 pbdagcon
    -rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 pbutgcns
    -rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 remove_fragment
    -rwxrwxr-x 1 urbe urbe 153K Apr 10 11:40 removeMateOverlap
    -rwxrwxr-x 1 urbe urbe 2,5K Apr 10 11:41 replaceUIDwithName-fastq
    -rwxrwxr-x 1 urbe urbe 1,2K Apr 10 11:41 replaceUIDwithName-posmap
    -rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 resolveSurrogates
    -rwxrwxr-x 1 urbe urbe 139K Apr 10 11:41 rewriteCache
    -rwxrwxr-x 1 urbe urbe 232K Apr 10 11:41 runCA
    -rwxrwxr-x 1 urbe urbe  88K Apr 10 11:41 runCA-dedupe
    -rwxrwxr-x 1 urbe urbe  14K Apr 10 11:41 runCA-overlapStoreBuild
    -rwxrwxr-x 1 urbe urbe 3,6K Apr 10 11:41 run_greedy.csh
    -rwxrwxr-x 1 urbe urbe 297K Apr 10 11:40 sffToCA
    -rwxrwxr-x 1 urbe urbe  13K Apr 10 11:40 show-corrects
    -rwxrwxr-x 1 urbe urbe 557K Apr 10 11:41 splitUnitigs
    -rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 terminator
    drwxrwxr-x 2 urbe urbe 4,0K Apr 10 11:41 TIGR
    -rwxrwxr-x 1 urbe urbe 526K Apr 10 11:41 tigStore
    -rwxrwxr-x 1 urbe urbe  35K Apr 10 11:41 tracearchiveToCA
    -rwxrwxr-x 1 urbe urbe  35K Apr 10 11:41 tracedb-to-frg.pl
    -rwxrwxr-x 1 urbe urbe  44K Apr 10 11:41 trimFastqByQVWindow
    -rwxrwxr-x 1 urbe urbe  18K Apr 10 11:40 uidclient
    -rwxrwxr-x 1 urbe urbe 589K Apr 10 11:41 unitigger
    -rwxrwxr-x 1 urbe urbe  42K Apr 10 11:40 upgrade-v8-to-v9
    -rwxrwxr-x 1 urbe urbe  42K Apr 10 11:40 upgrade-v9-to-v10
    -rwxrwxr-x 1 urbe urbe  854 Apr 10 11:41 utg2fasta
    -rwxrwxr-x 1 urbe urbe 731K Apr 10 11:41 utgcns
    -rwxrwxr-x 1 urbe urbe 561K Apr 10 11:41 utgcnsfix


    Address of the bookmark: http://wgs-assembler.sourceforge.net/wiki/index.php/Main_Page

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/37776/rhat-a-seed-and-extension-based-noisy-long-read-alignment-tool Sun, 23 Sep 2018 05:12:22 -0500 https://bioinformaticsonline.com/bookmarks/view/37776/rhat-a-seed-and-extension-based-noisy-long-read-alignment-tool <![CDATA[rHAT: a seed-and-extension-based noisy long read alignment tool]]> rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.

    Address of the bookmark: https://github.com/dfguan/rHAT

    ]]>     Abhimanyu Singh