<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43427?offset=430 https://bioinformaticsonline.com/bookmarks/view/44902/hite-a-fast-and-accurate-dynamic-boundary-adjustment-approach-for-full-length-transposable-elements-detection-and-annotation-in-genome-assemblies Sat, 20 Sep 2025 09:34:04 -0500 https://bioinformaticsonline.com/bookmarks/view/44902/hite-a-fast-and-accurate-dynamic-boundary-adjustment-approach-for-full-length-transposable-elements-detection-and-annotation-in-genome-assemblies <![CDATA[HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable Elements detection and annotation in Genome Assemblies]]> HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a greater number of full-length TEs.

panHiTE

We have developed panHiTE, a comprehensive and accurate pipeline for TE detection in large-scale population genomes. It has been successfully applied to hundreds of plant population genomes, demonstrating its effectiveness and scalability.

For detailed instructions, please refer to the panHiTE tutorial.

Address of the bookmark: https://github.com/CSU-KangHu/HiTE

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/41485/chromosight-computer-vision-based-program-for-pattern-recognition-in-chromosome-hi-c-contact-maps Mon, 23 Mar 2020 06:20:04 -0500 https://bioinformaticsonline.com/bookmarks/view/41485/chromosight-computer-vision-based-program-for-pattern-recognition-in-chromosome-hi-c-contact-maps <![CDATA[chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps]]> Python package to detect chromatin loops (and other patterns) in Hi-C contact maps.

Stable version with pip:

pip3 install --user chromosight

Stable version with conda:

conda install -c bioconda -c conda-forge chromosight

or, if you want to get the latest development version:

pip3 install --user -e git+https://github.com/koszullab/chromosight.git@master#egg=chromosight

Address of the bookmark: https://github.com/koszullab/Chromosight

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41405/sequence-tube-maps-displays-multiple-genomic-sequences-in-the-form-of-a-tube-map Wed, 11 Mar 2020 01:12:06 -0500 https://bioinformaticsonline.com/bookmarks/view/41405/sequence-tube-maps-displays-multiple-genomic-sequences-in-the-form-of-a-tube-map <![CDATA[Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map]]> A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)

Link to working demo: https://vgteam.github.io/sequenceTubeMap/

image

Address of the bookmark: https://github.com/vgteam/sequenceTubeMap

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