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MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other...
By Neel 2891 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 2699 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 2424 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 2240 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 1855 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 821 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...SRF Bioinformatics job position in National Institute of Plant Genome Research (NIPGR)
SRF Bioinformatics job position in National Institute of Plant Genome Research (NIPGR) Title : “Transcriptome and small RNA diversity analysis of developing seed contrasting rice varieties” Qualification : Candidates having M.Sc./M.Tech. degree...Phytozome v12.1: plant science community hub for accessing palnts genomic data
By Surabhi Chaudhary 2393 days agophytozome.jgi.doe.gov - Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as...
SPAdes hybrid genome assembly
Last updated 3234 days ago by Jit Comments (1)When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the...String graph based genome assembly software and tools !
By Rahul Nayak 3211 days agoIn graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication.
