Jit
Enthusiast computational biologist with business dream !!!
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Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences
By LEGE 399 days agogithub.com - Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3224 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 2438 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 1719 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...Ribbon !!
By Jit 3635 days agohttp://genomeribbon.com/ - Visualization has played an extremely important role in the current genomic revolution to inspect and understand variants, expression patterns, evolutionary changes, and a number of other relationships. However, most of the information in...gbtools: Interactive Visualization of Metagenome Bins in R
By Jit 3478 days agojournal.frontiersin.org - We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of...fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 3065 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...SVbyEye: R Package to visualize alignments between two or multiple DNA sequences
By LEGE 747 days agogithub.com - R Package to visualize alignments between two or multiple DNA sequences includinga number of functionalities to facilitate processing of alignments in PAF format. SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence...ACANA: An accurate and consistent alignment tool for DNA sequences
By Jit 3224 days agowww.niehs.nih.gov - ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts...DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
By Jit 3246 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...
