Jit
Enthusiast computational biologist with business dream !!!
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MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other...
By Neel 2242 days agogithub.com - An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to...multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
By Abhimanyu Singh 2050 days agogithub.com - multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 1775 days agogithub.com - This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 1591 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...JUDI: Just Do It
By Jit 1206 days agogithub.com - judi comes from the idea of bringing the power and efficiency of doit to execute any kind of task under many combinations of parameter settings. https://github.com/ncbi/JUDISqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 172 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...seqloc 0.6
By Gudiya Pal 3649 days agowww.stackage.org - The Bio.SeqLoc modules in seqloc are designed to represent positions and locations (ranges of positions) on sequences, particularly nucleotide sequences. My original motivation for writing these packages was handing the locations of genes in...SATSUMA : Highly sensitive whole-genome synteny alignments.
By Jit 3148 days agosatsuma.sourceforge.net - Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes,...Kraken: ultrafast metagenomic sequence classification using exact alignments
By Jit 3103 days ago Comments (1)www.ncbi.nlm.nih.gov - Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2841 days agoStructural variation caller tools using long reads
