s-aligner: a greedy algorithm for non-greedy de novo genome assembly

Genome assembly is a fundamental tool for biological research. Particularly, in microbiology, where budgets per sample are often scarce, it can make the difference between an inconclusive result and a fully valid conclusion. Identifying new strains or estimating the relative abundance of quasi-species in a sample are some example tasks that can’t be properly accomplished without previously generating assemblies with little structure ambiguity and covering most of the genome. In this work, we present a new genome assembly tool based on a greedy strategy. We compare the results obtained applying this tool to the results obtained with previously existing software. We find that, when applied to viral studies, comparatively, the software we developed often gets far larger contigs and higher genome fraction coverage than previous software. We also find a significant advantage when applied to exceptionally large virus genomes.

Efficient assembly of nanopore reads via highly accurate and intact error correction

Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.

Manual Shunt Connector Tool to Aid in No-Touch Technique

ABSTRACT BACKGROUND Given the morbidity and cost associated with cerebrospinal fluid shunt infections, many neurosurgical protocols implement “no-touch” technique to minimize infection. However, current surgical tools are not designed specifically for this task and surgeons often resort to using their hands to connect the shunt catheter to the valve. OBJECTIVE To develop an efficient and effective shunt assembly tool. METHODS Prototypes were designed using computer assisted software and machined in stainless steel. The amount of time and number of attempts it took volunteers to connect a Bacticel shunt catheter to a Delta valve were recorded using the new tool and standard shodded mosquitos. Scanning electron microscopy (SEM) was done on manipulated catheters to assess potential damage. Practicing neurosurgeons provided feedback. RESULTS Nonsurgeon (n = 13) volunteers and neurosurgeons (n = 6) both completed the task faster and with fewer attempts with the new tool (mean 7.18 vs 15.72 s and 2.00 vs 6.36 attempts, P < .0001; mean 2.93 vs 5.96 s and 1.06 vs 2.94 attempts, P < .001, respectively). SEM of 24 manipulated catheters showed no microscopic damage. 100% of neurosurgeons surveyed (n = 10) would adapt the tool in their practice, 90% preferred use of the new tool compared to their existing method, and 100% rated it easier to use compared to existing instruments. CONCLUSION The new tool shortened the time and number of attempts to connect a shunt catheter to a valve. Neurosurgeons preferred the new tool to existing instruments. There was no evidence of catheter damage with the use of this tool.

Haplotype-Resolved Assembly for Synthetic Long Reads Using a Trio-Binning Strategy

ABSTRACTThe accuracy and completeness of genome haplotyping are crucial for characterizing the relationship between human disease susceptibility and genetic variations, especially for the heterozygous variations. However, most of current variations are unphased genotypes, and the construction of long-range haplotypes remains challenging. We introduced a de novo haplotype-resolved assembly tool, HAST that exports two haplotypes of a diploid species for synthetic long reads with trio binning. It generates parental distinguishing k-mer libraries, partitions reads from the offspring according to the unique markers, and individually assembles them to resolve the haplotyping problem. Based on the stLFR co-barcoding data of an Asian as well as his parental massive parallel sequencing data, we utilized HAST to recover both haplotypes with a scaffold N50 of >11 Mb and an assembly accuracy of 99.99995% (Q63). The complete and accurate employment of long-range haplotyping information provided sub-chromosome level phase blocks (N50 ∼13 Mb) with 99.6% precision and 94.1% recall on average. We suggest that the accurate and efficient approach accomplishes the regeneration of the haplotype chromosomes with trio binning, thus promoting the determination of haplotype phase, the heterosis of crossbreeding, and the formation of autopolyploid and allopolyploid.

Fast and accurate assembly of Nanopore reads via progressive error correction and adaptive read selection

Although long Nanopore reads are advantageous in de novo genome assembly, applying Nanopore reads in genomic studies is still hindered by their complex errors. Here, we developed NECAT, an error correction and de novo assembly tool designed to overcome complex errors in Nanopore reads. We proposed an adaptive read selection and two-step progressive method to quickly correct Nanopore reads to high accuracy. We introduced a two-stage assembler to utilize the full length of Nanopore reads. NECAT achieves superior performance in both error correction and de novo assembly of Nanopore reads. NECAT requires only 7,225 CPU hours to assemble a 35X coverage human genome and achieves a 2.28-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line showed an NG50 of 29 Mbp. The high-quality assembly of Nanopore reads can significantly reduce false positives in structure variation detection.

Penyuluhan Dan Instalasi Kelistrikan Pada Mesin Pemisah Kulit Ari Kedelai UMKM Produksi Tempe Tradisional Di Desa Wringinpitu Banyuwangi

Problems found in related to electrical installations in buildings/houses are not arranged perfectly or the installation is not following to the procedure because there have been improvements to the electrical installations of the building or house beforehand. Electrical installations that will be installed should also consider the concept of savings and costs Installation and addition of electrical installations with equipment that is not based on knowledge of electrical installations can be dangerous if not carried out by save maintenance and security of existing electrical equipment. Based on the situation analysis of MSME traditional tempe producers that have a separator machine using an electric motor, there is a need for a good and correct electrical installation to prevent the user avoid from electrical shock that could be potentially dangerous, because the separator from the soybean skin is a direct contact with water. The method of implementation in community service activities at Tempe producers MSMEs include; Field Observation, Tool Design, Tool Assembly, Tool Testing, Tool Installation, Electricity Installation, Electricity and Operation Training, and MONEV. The results of a series of community service activities that have been carried out are being able to increase the knowledge of all who are on the business purposes to understand how electricity and good installation are save from an unwanted thing about electricity.

Assembly Tool Manufacturing and Optimization for Polylactic Acid Additive Manufacturing

Paper focuses on additive manufacturing of assembly tool for hole selection. One of the most important part in design and optimization process in additive manufacturing for assembly tool is material selection and technology. In this case was chosen plastic material know as poly-lactic-acid. Polylactic acid has low shrinkage and huge potential in assembly tooling and assembly fixture manufacturing. Main benefits are in use of additive manufacturing for this purpose because of huge manufacturing variability and time savings in case of frequent design changes. From filament fused fabrication technology stand point is important to determine right manufacturing orientation of part. Main material benefit is bio-degradability and recyclability. Current trend in manufacturing is bio materials, clean manufacturing and ecofriendly products. Correct orientation of assembly tool will optimize manufacturing process in one way. Article is aimed on manufacturing precision in each orientation of part on build late. With right orientation of part in additive manufacturing process is determined exact precision of assembly tool manufacturing. For measurement was used coordinate-measuring machine. In this case measurements and precision checking are made only in exact spots where is needed the most precise distance