<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38277?offset=20 https://bioinformaticsonline.com/bookmarks/view/37563/colormap-correcting-long-reads-by-mapping-short-reads Mon, 20 Aug 2018 14:17:05 -0500 https://bioinformaticsonline.com/bookmarks/view/37563/colormap-correcting-long-reads-by-mapping-short-reads <![CDATA[CoLoRMap: Correcting Long Reads by Mapping short reads]]> Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage. This motivates the development of hybrid approaches that leverage the high quality of short reads to correct errors in long reads.We introduce CoLoRMap, a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence of overlapping short reads that minimizes the edit score to a long read and extending corrected regions by local assembly of unmapped mates of mapped short reads. Our results on bacterial, fungal and insect data sets show that CoLoRMap compares well with existing hybrid correction methods.The source code of CoLoRMap is freely available for non-commercial use at https://github.com/sfu-compbio/colormap

ehaghshe@sfu.ca or cedric.chauve@sfu.ca

Address of the bookmark: https://github.com/sfu-compbio/colormap

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37509/vcftools-perform-common-tasks-with-vcf-files-such-as-file-validation-file-merging-intersecting-complements Tue, 07 Aug 2018 10:01:46 -0500 https://bioinformaticsonline.com/bookmarks/view/37509/vcftools-perform-common-tasks-with-vcf-files-such-as-file-validation-file-merging-intersecting-complements <![CDATA[VCFtools: perform common tasks with VCF files such as file validation, file merging, intersecting, complements]]> VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. The Perl tools support all versions of the VCF specification (3.2, 3.3, 4.0, 4.1 and 4.2), nevertheless, the users are encouraged to use the latest versions VCFv4.1 or VCFv4.2. The VCFtools in general have been used mainly with diploid data, but the Perl tools aim to support polyploid data as well. Run any of the Perl scripts with the --help switch to obtain more help.

Many of the Perl scripts require that the VCF files are compressed by bgzip and indexed by tabix (both tools are part of the tabix package, available for download here). The VCF files can be compressed and indexed using the following commands

bgzip my_file.vcf
tabix -p vcf my_file.vcf.gz

 

http://vcftools.sourceforge.net/perl_module.html

Address of the bookmark: http://vcftools.sourceforge.net/perl_module.html

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/31105/understanding-pacbio Fri, 24 Feb 2017 10:17:36 -0600 https://bioinformaticsonline.com/bookmarks/view/31105/understanding-pacbio <![CDATA[Understanding PacBio]]> This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you get started with your data processing, as well as information for specialized applications.

Training Resources:

Specialized Applications:

Address of the bookmark: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/32190/dbg2olcefficient-assembly-of-large-genomes-using-long-erroneous-reads-of-the-third-generation-sequencing-technologies Wed, 19 Apr 2017 10:09:51 -0500 https://bioinformaticsonline.com/bookmarks/view/32190/dbg2olcefficient-assembly-of-large-genomes-using-long-erroneous-reads-of-the-third-generation-sequencing-technologies <![CDATA[DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies]]> DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

Our work is published in Scientific Reports:

Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci. Rep. 6, 31900; doi: 10.1038/srep31900 (2016).

http://www.nature.com/articles/srep31900

The manual can be downloaded from:

https://github.com/yechengxi/DBG2OLC/raw/master/Manual.docx

To use precompiled versions,please go to:

https://github.com/yechengxi/DBG2OLC/tree/master/compiled

 

Address of the bookmark: https://github.com/yechengxi/DBG2OLC

]]> 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