Jit
Enthusiast computational biologist with business dream !!!
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multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
By Abhimanyu Singh 2018 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 1743 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 1558 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 1174 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 140 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 3617 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 3115 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 3070 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 2809 days agoStructural variation caller tools using long readsFOGSAA: Fast Optimal Global Sequence Alignment Algorithm
By Jit 2541 days agowww.isical.ac.in - Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a...
