<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37457?offset=480 https://bioinformaticsonline.com/bookmarks/view/39671/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads Sat, 06 Jul 2019 03:48:22 -0500 https://bioinformaticsonline.com/bookmarks/view/39671/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads <![CDATA[Flye: Fast and accurate de novo assembler for single molecule sequencing reads]]> Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

Address of the bookmark: https://github.com/fenderglass/Flye

]]> Rahul Nayak 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/42271/mcclintock-meta-pipeline-to-identify-transposable-element-insertions-using-next-generation-sequencing-data Tue, 27 Oct 2020 00:21:18 -0500 https://bioinformaticsonline.com/bookmarks/view/42271/mcclintock-meta-pipeline-to-identify-transposable-element-insertions-using-next-generation-sequencing-data <![CDATA[McClintock: Meta-pipeline to identify transposable element insertions using next generation sequencing data]]> an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae. 

Address of the bookmark: https://github.com/bergmanlab/mcclintock

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44659/figeno-tool-for-plotting-sequencing-data-along-genomic-coordinates Tue, 17 Sep 2024 02:28:15 -0500 https://bioinformaticsonline.com/bookmarks/view/44659/figeno-tool-for-plotting-sequencing-data-along-genomic-coordinates <![CDATA[Figeno: Tool for plotting sequencing data along genomic coordinates.]]> Tool for plotting sequencing data along genomic coordinates.

FIGENO is a
  FIGure
    GENerator
for GENOmics

With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview: https://www.youtube.com/watch?v=h1cBeXoSYTA.

figeno

Address of the bookmark: https://github.com/CompEpigen/figeno

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