Jit
Enthusiast computational biologist with business dream !!!
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MUMmer4: A fast and versatile genome alignment system
By Jit 2484 days agomummer4.github.io - MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing...GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2372 days ago1001genomes.org - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2299 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...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2252 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)...Caretta – A multiple protein structure alignment and feature extraction suite
By Rahul Nayak 1435 days agowww.bioinformatics.nl - Caretta – a multiple protein structure alignment and feature extraction suite Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments...DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
By Jit 2564 days agohttps://dfast.nig.ac.jp/ - We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its...jobTree based python wrapper to run the genome simulation tool suite Evolver
By Jit 2540 days agogithub.com - evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation...NovoGraph: building whole genome graphs from long-read-based de novo assemblies
By Jit 2198 days agogithub.com - NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 1757 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...VCF Compare !
By Rahul Nayak 1037 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...
