<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/11365?offset=40 https://bioinformaticsonline.com/bookmarks/view/38304/lordfast-sensitive-and-fast-alignment-search-tool-for-long-noisy-read-sequencing-data Tue, 27 Nov 2018 04:43:57 -0600 https://bioinformaticsonline.com/bookmarks/view/38304/lordfast-sensitive-and-fast-alignment-search-tool-for-long-noisy-read-sequencing-data <![CDATA[lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data]]> lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

 

Address of the bookmark: https://github.com/vpc-ccg/lordfast

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data Tue, 22 Jan 2019 06:26:55 -0600 https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data <![CDATA[Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data]]>
  • Run a pipeline processing fast5s to a consensus in a single command.
  • Recommended fixed "standard" and "fast" pipelines.
  • Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
  • Seemless distribution of tasks over local or distributed compute.
  • Highly configurable.
  • Open source (Mozilla Public License 2.0).

    • Documentation can be found at https://nanoporetech.github.io/katuali/.

    Address of the bookmark: https://github.com/nanoporetech/katuali

    ]]>     Jit     https://bioinformaticsonline.com/researchlabs/view/39827/prof-dr-med-andreas-ramming Wed, 07 Aug 2019 03:25:48 -0500 <![CDATA[Prof. Dr. med. Andreas Ramming]]> In many autoimmune diseases, a misdirected immune response leads to chronic inflammation and subsequently to fibrotic and degenerative tissue remodeling. Therapeutic options are available for inflammatory joint diseases, but only about 40% of patients respond to these existing therapies on a permanent basis. In the remaining cases, these therapies miss their target from the beginning or later during the course of treatment failure. There are currently no causal therapies available for the treatment of fibrotic autoimmune diseases such as systemic sclerosis. Therefore, there is an urgent need to develop new therapeutic options for the treatment of fibrotic and synovitic autoimmune diseases. His group is therefore deal with the molecular mechanisms of these misdirected signaling pathways for the development of novel, targeted therapies

    http://www.medizin3.uk-erlangen.de/forschung/arbeitsgruppen/matrixbiologie-entzuendliche-signalwege-in-arthritis-und-fibrose/

    ]]>         https://bioinformaticsonline.com/bookmarks/view/40701/fastgt-an-alignment-free-method-for-calling-common-snvs-directly-from-raw-sequencing-reads Tue, 28 Jan 2020 03:27:33 -0600 https://bioinformaticsonline.com/bookmarks/view/40701/fastgt-an-alignment-free-method-for-calling-common-snvs-directly-from-raw-sequencing-reads <![CDATA[FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads]]> FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the frequency of k-mers in sequencing data and predicts the genotype. All this takes less than 1 hour on average low-cost Linux server.

    http://bioinfo.ut.ee/FastGT/

    https://github.com/bioinfo-ut/GenomeTester4/

    Address of the bookmark: http://bioinfo.ut.ee/FastGT/

    ]]>     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/42826/ktrim-an-extra-fast-and-accurate-adapter-and-quality-trimmer-for-sequencing-data Thu, 11 Feb 2021 21:39:05 -0600 https://bioinformaticsonline.com/bookmarks/view/42826/ktrim-an-extra-fast-and-accurate-adapter-and-quality-trimmer-for-sequencing-data <![CDATA[Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data]]> Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz v1.2.7 for Linux x86_64 system. If you could not run it (which is usually caused by low version of libc++ or libz library) or you want to build a version optimized for your system, you can re-compile the programs:

    user@linux$ make clean && make

    Address of the bookmark: https://github.com/hellosunking/Ktrim

    ]]>     Jit     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/opportunity/view/24178/essentials-of-statistics-and-data-analysis-using-r Mon, 31 Aug 2015 01:32:12 -0500 <![CDATA[Essentials of Statistics and Data Analysis using R]]> Clinical Development Services Agency (CDSA) is an extramural unit of Translational Health Science and Technology Institute (THSTI), Department of Biotechnology, Ministry of Science & Technology, Government of India. CDSA has a national mandate of strengthening capacity and capability building in the area of Clinical development and Translational Research.

    CDSA is pleased to announce a 4 days hands-on training program on “Essentials of Statistics and Data Analysis using R” at ICGEB, Aruna Asaf Ali Road, New Delhi on December 1 – 4, 2015. This will involve developing and enhancing skills to understand basic principles of statistics for summarizing data and use of appropriate statistical tests as well as providing an understanding of data analysis using R. Didactic lectures with practical sessions will be delivered by experienced faculties from AIIMS and Novartis. Live classroom with power point presentations, case studies, mock exercise, practical sessions on R, group work with time for discussion and Q&A sessions are added advantages of this workshop.

    Please contact gayatrivishwakarma.cdsa@thsti.res.in or vineetabaloni.cdsa@thsti.res.in for program and registration details.

    Please nominate personage or register yourself on or before November 6, 2015 along with the electronic transfer of registration fee.

    ]]>         https://bioinformaticsonline.com/bookmarks/view/41144/seqmule-automated-human-exomegenome-variants-detection Tue, 18 Feb 2020 03:22:54 -0600 https://bioinformaticsonline.com/bookmarks/view/41144/seqmule-automated-human-exomegenome-variants-detection <![CDATA[SeqMule: Automated human exome/genome variants detection]]> SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.

    Address of the bookmark: https://doc-openbio.readthedocs.io/projects/seqmule/en/latest/

    ]]>     BioStar     https://bioinformaticsonline.com/opportunity/view/4728/3-days-intensive-course-on-understanding-omics-data-in-basel-switzerland-19-21st-november Mon, 23 Sep 2013 10:46:57 -0500 <![CDATA[3 days intensive course on Understanding 'omics data in Basel, Switzerland, 19-21st November]]> Benefits for the participants

    - Plan more efficient experiments
    - Correctly interpret results
    - Communicate results in publications more effectively

    The course focus is on methodologies, not on particular software tools. After the course participants should be able to apply the methods in their respective environment. However, during the course, hands-on sessions will be performed using the Genedata Expressionist® software, which enables participants to quickly apply the discussed methods and visualize results. No previous knowledge on Expressionist® is required; access to the software is free of charge during the course.

    More @ http://www.dixa-fp7.eu/dixa-training/dixa-training-agenda/genedata-academy#!

    ]]>