Shruti Paniwala
A Bioinformatician
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JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
By Jit 1711 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wikiJCVI utility libraries
By Jit 1293 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.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...CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
By Shruti Paniwala 1471 days agogitlab.gwdg.de - CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2374 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...BLAST options, setting and defaults
By Jit 2174 days agowww.arabidopsis.org - BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA...npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
By Jit 2740 days agogithub.com - npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It...WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.
By Neel 1156 days agohuttenhower.sph.harvard.edu - Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2383 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...GFinisher: a new strategy to refine and finish bacterial genome assemblies
By Jit 2311 days agogfinisher.sourceforge.net - GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar...
