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DIAL
By Abhimanyu Singh 3505 days agowww.bx.psu.edu - A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...funannotate: Eukaryotic Genome Annotation Pipeline
By Jit 2938 days agogithub.com - Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this...Basic Structure of Snakemake Pipeline Run !
By Abhi 1817 days agoBrief Overview of Snakemake Pipeline CommandsBioinformatician in pipeline development
Are you interested in working with pipeline development in bioinformatics, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers...Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
By Jit 3238 days agosourceforge.net - Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the...ARC: pipeline which facilitates iterative, reference guided de novo assemblies
By Jit 2993 days agoibest.github.io - ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble...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/JUDI
