Our Sponsors
Related items
Opera: An optimal genome scaffolding program
By Jit 2531 days agosourceforge.net - Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from...
SPAdes hybrid genome assembly
Last updated 2531 days ago by Jit Comments (1)When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 2522 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...-
Tools for bacterial whole genome annotation
Last updated 2511 days ago by Radha AgarkarRAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation... Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole...
By Jit 2501 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...-
List of visualization tools for genome alignments
Last updated 2463 days ago by Rahul NayakGenome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which... G-compass: a comparative genome browser
By Jit 2395 days agowww.h-invitational.jp - G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2)....Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2362 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...PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
By Surabhi Chaudhary 2335 days agoderisilab.ucsf.edu - We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively...KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
By Jit 2310 days ago Comments (1)github.com - KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in...
