<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/32948?offset=40 https://bioinformaticsonline.com/bookmarks/view/34328/dfast-a-flexible-prokaryotic-genome-annotation-pipeline-for-faster-genome-publication Tue, 14 Nov 2017 10:26:16 -0600 https://bioinformaticsonline.com/bookmarks/view/34328/dfast-a-flexible-prokaryotic-genome-annotation-pipeline-for-faster-genome-publication <![CDATA[DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication]]> We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability and Implementation

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39450/apollo-first-instantaneous-collaborative-genomic-annotation-editor-available-on-the-web Fri, 31 May 2019 19:55:39 -0500 https://bioinformaticsonline.com/bookmarks/view/39450/apollo-first-instantaneous-collaborative-genomic-annotation-editor-available-on-the-web <![CDATA[Apollo: First instantaneous, collaborative genomic annotation editor available on the Web]]>
  • Apollo is a plug-in for the JBrowse Genome Viewer.
  • In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the ‘Information Editor’.
  • History tracking with undo/redo functions is available.
  • Users are able to directly set an annotation to a specific state, choosing from the ‘History’ display.
  • Adding and updating PubMed IDs will prompt users with a publication title to confirm their submission.
  • Gene Ontology (GO) terms are supported and GO ID auto-completion has been incorporated.
  • Users may access a ‘Recent Changes’ page.
  • Help page with Apollo specific content is available.

    • Address of the bookmark: http://genomearchitect.github.io/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/43711/vcf-compare Wed, 19 Jan 2022 10:30:14 -0600 https://bioinformaticsonline.com/bookmarks/view/43711/vcf-compare <![CDATA[VCF Compare !]]> compare two BWA mapping methods with the online hg18-mapped data

    We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/NA18507_GAIIx_100_chr21.bam>, aligned to the b36/hg18 reference genome)

    Address of the bookmark: https://wiki.bits.vib.be/index.php/NGS_Exercise.6#compare_aln_.26_mem_results_with_vcf-compare

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/bookmarks/view/43801/smudgeplot-inference-of-ploidy-and-heterozygosity-structure-using-whole-genome-sequencing-data Fri, 25 Feb 2022 04:42:09 -0600 https://bioinformaticsonline.com/bookmarks/view/43801/smudgeplot-inference-of-ploidy-and-heterozygosity-structure-using-whole-genome-sequencing-data <![CDATA[Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data]]> This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.

    Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:

    smudgeexample

    Address of the bookmark: https://github.com/KamilSJaron/smudgeplot

    ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/43867/genomeqc-a-quality-assessment-tool-for-genome-assemblies-and-gene-structure-annotations Thu, 19 May 2022 04:29:05 -0500 https://bioinformaticsonline.com/bookmarks/view/43867/genomeqc-a-quality-assessment-tool-for-genome-assemblies-and-gene-structure-annotations <![CDATA[GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations]]> The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.

    https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2

    Address of the bookmark: https://github.com/HuffordLab/GenomeQC

    ]]>     Neel     https://bioinformaticsonline.com/file/view/19560/alien-genome Sat, 13 Dec 2014 00:24:32 -0600 https://bioinformaticsonline.com/file/view/19560/alien-genome <![CDATA[Alien Genome !!!]]> Genome sequencing, analysis and expression of Alien genome.

    Note: This image/cartoon is create only for fun. It has nothing to do with any scientific findings.

    ]]>     Jit     https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome Thu, 08 Aug 2024 23:31:18 -0500 https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome <![CDATA[Tools to access the quality of your assembled genome !]]>
  • FASTA VALIDATOR + SEQKIT RMDUP: FASTA validation
  • GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation
  • ASSEMBLATHON STATS: Assembly statistics
  • GENOMETOOLS GT STAT: Annotation statistics
  • NCBI FCS ADAPTOR: Adaptor contamination pass/fail
  • NCBI FCS GX: Foreign organism contamination pass/fail
  • BUSCO: Gene-space completeness estimation
  • TIDK: Telomere repeat identification
  • LAI: Continuity of repetitive sequences
  • KRAKEN2: Taxonomy classification
  • HIC CONTACT MAP: Alignment and visualisation of HiC data
  • MUMMER → CIRCOS + DOTPLOT & MINIMAP2 → PLOTSR: Synteny analysis
  • MERQURY: K-mer completeness, consensus quality and phasing assessment
    • ]]>     LEGE     https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines Wed, 15 Jun 2016 17:18:36 -0500 https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines <![CDATA[LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines]]> LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.

    Publication:

    • L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016.

    Download:

    Address of the bookmark: https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/35420/telomerehunter Fri, 02 Feb 2018 04:23:59 -0600 https://bioinformaticsonline.com/bookmarks/view/35420/telomerehunter <![CDATA[TelomereHunter]]> TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as input. However, it is also possible to run TelomereHunter with one input file. TelomereHunter extracts and sorts telomeric reads from the input sample(s). For the estimation of telomere content, GC biases are taken into account. Finally, the results of TelomereHunter are visualized in several diagrams.

    TelomereHunter is available for download at the following address: https://pypi.python.org/pypi/telomerehunter/

    Address of the bookmark: http://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/37496/gsearch-a-fast-and-flexible-general-search-tool-for-whole-genome-sequencing Mon, 06 Aug 2018 17:19:15 -0500 https://bioinformaticsonline.com/bookmarks/view/37496/gsearch-a-fast-and-flexible-general-search-tool-for-whole-genome-sequencing <![CDATA[gSearch: a fast and flexible general search tool for whole-genome sequencing]]> gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner. 

    Address of the bookmark: http://ml.ssu.ac.kr/gSearch/index.html

    ]]>     Jit