Results for "Sequence"
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Kalign: fast multiple sequence alignment program for biological sequences.
Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal format: kalign -i BB11001.tfa -f clu -o out.clu Re-align seq...Tags: Kalign, fast, multiple, sequence, alignment, biological, sequences
1641 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
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 to significantly reduce the execution time of sho...Tags: Shouji, fast, efficient, pre-alignment, filter, sequence, alignment
1637 days ago
RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing info...Tags: RePS, Repeat, masked, Phrap, scaffolding, WGS, sequence, assembler
1577 days ago
GfaViz: flexible and interactive visualization of GFA sequence graphs
GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general, and able to represent many different types of sequ...Tags: GfaViz, flexible, interactive, visualization, GFA, sequence, graphs
1557 days ago
Complete genome sequence of Wuhan seafood market pneumonia virus is out !
Wuhan-Hu-1 claimed at least 40 lives and infected at least 1300 others in China. Cases are now being reported from Thailand, Singapore, Malaysia, South Korea, Japan, Vietnam, Nepal, France, Australia and even as far as the US. On Jan 10 2020, while news of the first fatality was barely trick...Tags: Complete, genome, sequence, Wuhan, seafood, market, pneumonia, virus, MN908947
1549 days ago
- AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguish...
Tags: AccessSyRI, finding, genomic, rearrangements, sequence, differences, whole-genome, assemblies
1548 days ago
CLARK: Fast, accurate and versatile sequence classification system
CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial genomes, and (2) the assignment ...Tags: CLARK, Fast, accurate, versatile, sequence, classification, system, bacteria
1535 days ago
LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usua...Tags: LoFreq, sequence, quality, aware, ultra-sensitive, variant, caller, NGS, data
1531 days ago
China’s BGI says it can sequence a genome for just $100
Using technology originally acquired in the US, the Chinese gene giant BGI Group says it will make genome sequencing cheaper than ever, breaking the $100 barrier for the first time. The Shenzhen company says the low cost will be possible with an “extreme” DNA sequencing system it pla...Tags: China, BGI, sequence, genome, $100
1520 days ago
Submit your SARS-CoV-2 sequence data to GenBank
Submit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page. Submission is simple and streamlined *and* there’s a rapid turnaround. https://submit.ncbi.nlm.nih.gov/sarscov2/ Quickly and easily add your SARS-CoV-2 sequence data to the growing public ...Tags: Submit, SARS-CoV-2, sequence, data, GenBank, CoVID-19 Covid, Virus
1480 days ago
