<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34501?offset=310 https://bioinformaticsonline.com/bookmarks/view/11175/next-generation-sequencingngs-books Fri, 30 May 2014 04:48:04 -0500 https://bioinformaticsonline.com/bookmarks/view/11175/next-generation-sequencingngs-books <![CDATA[Next generation sequencing(NGS) books]]> Employing different technologies, the purpose of NGS platform is to decode the identity or modification on the nucleotides. NGS platforms evolve quickly and capture the main stream.

This bookmark is created to provide NGS online books links.

Address of the bookmark: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Print_version

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/34394/tulip-the-uncorrected-long-read-itegration-pipeline Thu, 23 Nov 2017 09:30:01 -0600 https://bioinformaticsonline.com/bookmarks/view/34394/tulip-the-uncorrected-long-read-itegration-pipeline <![CDATA[TULIP - The Uncorrected Long read Itegration Pipeline]]> #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel)

TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow. 
Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures. Tulipbulb adds long read sequencing data to these.

 

https://github.com/Generade-nl/TULIP

Address of the bookmark: https://github.com/Generade-nl/TULIP

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39903/integrative-meta-assembly-pipeline-imap-chromosome-level-genome-assembler-combining-multiple-de-novo-assemblies Sat, 31 Aug 2019 11:30:41 -0500 https://bioinformaticsonline.com/bookmarks/view/39903/integrative-meta-assembly-pipeline-imap-chromosome-level-genome-assembler-combining-multiple-de-novo-assemblies <![CDATA[Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies]]> Chromosome-level genome assembler combining multiple de novo assemblies

https://github.com/jkimlab/IMAP

Address of the bookmark: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0221858

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44470/phyloherb-phylogenomic-analysis-pipeline-for-herbarium-specimens Wed, 21 Feb 2024 06:15:13 -0600 https://bioinformaticsonline.com/bookmarks/view/44470/phyloherb-phylogenomic-analysis-pipeline-for-herbarium-specimens <![CDATA[PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens]]> What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a species tree. It is designed to be a high throughput program dealing with lower quality data. Examples include low-coverage (5x cpDNA) plastome phylogeny, recycling plastid genes from target enrichment data, retrieving low-copy nuclear genes from medium coverage (5x nucDNA) genome skimming.

Address of the bookmark: https://github.com/lmcai/PhyloHerb/

]]> LEGE https://bioinformaticsonline.com/blog/view/45249/from-dna-chaos-to-a-clear-microbial-story Fri, 21 Aug 2026 11:22:54 -0500 https://bioinformaticsonline.com/blog/view/45249/from-dna-chaos-to-a-clear-microbial-story <![CDATA[From DNA Chaos to a Clear Microbial Story]]> Imagine opening a metagenomic dataset and finding millions of DNA fragments, each carrying a tiny piece of information about the microbial world inside a sample. The challenge is not generating the data — it is turning that data into a meaningful story.

This is where MeTAline comes in.

MeTAline is a reproducible workflow designed to simplify shotgun metagenomic analysis. It brings together important steps such as quality control, host-DNA removal, taxonomic profiling and functional analysis, using tools including Kraken2, MetaPhlAn4 and HUMAnN.

What makes it especially useful is its ability to handle large datasets while keeping analyses organized and reproducible. Built with Snakemake and supporting containerized environments, MeTAline can also be used on high-performance computing systems.

In simple terms, MeTAline helps researchers move from millions of confusing DNA fragments to a clearer picture of who is there, what they might be doing, and what the data could mean.

Sometimes, the biggest challenge in science isn't collecting more data — it's finding the story hidden inside it.

Read more at https://academic.oup.com/nargab/article/7/4/lqaf158/8340158?login=false

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/35292/pgap-x-extension-on-pan-genome-analysis-pipeline Tue, 23 Jan 2018 11:41:43 -0600 https://bioinformaticsonline.com/bookmarks/view/35292/pgap-x-extension-on-pan-genome-analysis-pipeline <![CDATA[PGAP-X: Extension on pan-genome analysis pipeline]]> PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different conservative levels, and genetic variation from pan-genome sight. At the same time, analytical result data from many other programs, including genome alignment result and orthologs clusters, are also supported to be further analyzed or visualized in PGAP-X. The workflow and feature snapshot in PGAP-X were shown as Fig.1 and Fig.2.

image
 

 

Address of the bookmark: https://pgapx.ybzhao.com/

]]> Rahul Nayak 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/bookmarks/view/40611/deepvariant-an-analysis-pipeline-that-uses-a-deep-neural-network-to-call-genetic-variants-from-next-generation-dna-sequencing-data Sat, 25 Jan 2020 13:28:09 -0600 https://bioinformaticsonline.com/bookmarks/view/40611/deepvariant-an-analysis-pipeline-that-uses-a-deep-neural-network-to-call-genetic-variants-from-next-generation-dna-sequencing-data <![CDATA[DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.]]> DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

    DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant relies on Nucleus, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the TensorFlow machine learning framework.

    https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html

    https://www.biorxiv.org/content/10.1101/092890v6

    image

    Address of the bookmark: https://github.com/google/deepvariant

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/41998/wgddetector-a-pipeline-for-detecting-whole-genome-duplication-events-using-the-genome-or-transcriptome-annotations Thu, 23 Jul 2020 05:52:56 -0500 https://bioinformaticsonline.com/bookmarks/view/41998/wgddetector-a-pipeline-for-detecting-whole-genome-duplication-events-using-the-genome-or-transcriptome-annotations <![CDATA[WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations]]> WGDdetector pipeline that integrates all analyses including gene family constructing, dS estimating and phasing, and outputting the dS values of each paralogs pairs processed with only one command. We further chose four species (Arabidopsis thaliana, Juglans regia, Populus trichocarpa and Xenopus laevis) representing herb, wood and animal, to test its practicability. Our final results showed a high degree of accuracy with the previous studies using both genome and transcriptome data.

    More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2670-3

    Address of the bookmark: https://github.com/yongzhiyang2012/wgddetector

    ]]>     LEGE     https://bioinformaticsonline.com/bookmarks/view/42946/aligngraph2-similar-genome-assisted-reassembly-pipeline-for-pacbio-long-reads Sun, 14 Mar 2021 09:42:47 -0500 https://bioinformaticsonline.com/bookmarks/view/42946/aligngraph2-similar-genome-assisted-reassembly-pipeline-for-pacbio-long-reads <![CDATA[AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads]]> AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.

    More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/6146772

    Address of the bookmark: https://github.com/huangs001/AlignGraph2

    ]]>     Rahul Nayak