<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43090?offset=490 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/40460/sviper-swipe-your-structural-variants-called-on-long-ontpacbio-reads-with-short-exact-illumina-reads Sun, 22 Dec 2019 03:48:28 -0600 https://bioinformaticsonline.com/bookmarks/view/40460/sviper-swipe-your-structural-variants-called-on-long-ontpacbio-reads-with-short-exact-illumina-reads <![CDATA[SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.]]> Call sviper

    ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants

    This will output a polished_variants.vcf file, that contains all the refined variants.

    Sometimes it is helpful to look at the polished sequence, e.g. with the IGV browser. In that case you want SViper to output the polished and aligned sequences in a bam file via the option --output-polished-bam:

    ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants --output-polished-bam

    Address of the bookmark: https://github.com/smehringer/SViper

    ]]>     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/19980/seqloc-06 Sun, 28 Dec 2014 12:51:29 -0600 https://bioinformaticsonline.com/bookmarks/view/19980/seqloc-06 <![CDATA[seqloc 0.6]]> The Bio.SeqLoc modules in seqloc are designed to represent positions and locations (ranges of positions) on sequences, particularly nucleotide sequences. My original motivation for writing these packages was handing the locations of genes in eukaryotic genomes.

    Handle sequence locations for bioinformatics http://www.ingolia-lab.org/seqloc-tutorial.html

    Address of the bookmark: http://www.stackage.org/snapshot/nightly-2014-12-28/package/seqloc-0.6

    ]]>     Gudiya Pal     https://bioinformaticsonline.com/bookmarks/view/27333/satsuma-highly-sensitive-whole-genome-synteny-alignments Fri, 13 May 2016 05:25:26 -0500 https://bioinformaticsonline.com/bookmarks/view/27333/satsuma-highly-sensitive-whole-genome-synteny-alignments <![CDATA[SATSUMA : Highly sensitive whole-genome synteny alignments.]]> Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.

    Satsuma has parallelization built-in and is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs.

    You can find the manual here.
    Download the latest source code from here.
    Stable versions can also be downloaded from the Broad Institute's web site.

    An incomplete list of questions and answers (yes, these have really been asked by our users! Please feel free to add your own by e-mailing us) is here.

    If you use Satsuma in your research, please cite:
    Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.

    Tutorial at http://evomics.org/learning/genomics/satsuma/

    Address of the bookmark: http://satsuma.sourceforge.net/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/28119/kraken-ultrafast-metagenomic-sequence-classification-using-exact-alignments Mon, 27 Jun 2016 11:01:44 -0500 https://bioinformaticsonline.com/bookmarks/view/28119/kraken-ultrafast-metagenomic-sequence-classification-using-exact-alignments <![CDATA[Kraken: ultrafast metagenomic sequence classification using exact alignments]]> Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.

    Krona

    https://sourceforge.net/p/krona/home/krona/

    Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053813/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/33479/novelseq-novel-sequence-insertion-detection Fri, 09 Jun 2017 04:31:30 -0500 https://bioinformaticsonline.com/bookmarks/view/33479/novelseq-novel-sequence-insertion-detection <![CDATA[NovelSeq: Novel Sequence Insertion Detection]]> The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

    http://novelseq.sourceforge.net/Home

    Paper at https://www.ncbi.nlm.nih.gov/pubmed/20385726

    Address of the bookmark: http://novelseq.sourceforge.net/Home

    ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r Mon, 09 Jul 2018 05:20:50 -0500 https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r <![CDATA[ASAR: Advanced metagenomic Sequence Analysis in R]]> An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

    To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

    Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/42359/dnasp-dna-sequence-polymorphism-is-a-software-package-for-the-analysis-of-dna-polymorphisms Wed, 25 Nov 2020 19:51:38 -0600 https://bioinformaticsonline.com/bookmarks/view/42359/dnasp-dna-sequence-polymorphism-is-a-software-package-for-the-analysis-of-dna-polymorphisms <![CDATA[DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms]]> DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software). DnaSP can estimate several measures of DNA sequence variation within and between populations in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.

    Address of the bookmark: http://www.ub.edu/dnasp/

    ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/44555/ultra-ultra-locates-tandemly-repetitive-areas-effective-labeling-of-repetitive-genomic-sequence Sat, 08 Jun 2024 16:03:39 -0500 https://bioinformaticsonline.com/bookmarks/view/44555/ultra-ultra-locates-tandemly-repetitive-areas-effective-labeling-of-repetitive-genomic-sequence <![CDATA[ULTRA (ULTRA Locates Tandemly Repetitive Areas) : Effective Labeling of Repetitive Genomic Sequence]]> ULTRA is a tool to find and annotate tandem repeats inside genomic sequence. It is able to find repeats of any length and of any period (up to a maximum period of 4000). It can find highly decayed repeats missed by other software, and it will also be able to find very large repeats in highly repetitive sequence, regardless of the size of sequence or length of repeats. ULTRA offers meaningful annotation scores and can produce annotation P-values at user request.

    More at https://www.biorxiv.org/content/10.1101/2024.06.03.597269v1

    Address of the bookmark: https://github.com/TravisWheelerLab/ULTRA

    ]]>     Abhi