Radha Agarkar
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Prokka: tool for the rapid annotation of prokaryotic genomes
By Jit 3289 days agowww.vicbioinformatics.com - Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2770 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...COCACOLA (binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and...
By Jit 3288 days agogithub.com - COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs. Furthermore,...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2723 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...sequenceserver
By Jit 3285 days agogithub.com - SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web. More at http://sequenceserver.com.Shouji: a fast and efficient pre-alignment filter for sequence alignment
By Jit 2316 days agogithub.com - The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3279 days agoStructural variation caller tools using long readsFools guide
By Poonam Mahapatra 3261 days agosfg.stanford.edu - This website and accompaning documents are intended as a tool to help researchers dealing with non-model organisms acquire and process transcriptomic high-throughput sequencing data without having to learn extensive bioinformatics skills. It covers...LoRDEC: a hybrid error correction program for long, PacBio reads
By Jit 3254 days agowww.atgc-montpellier.fr - LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read...
