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SPAdes
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A single-cell assembler for capturing and sequencing “microbial dark matter” that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes from the mini-metagenome at once. SPAdes is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide Additional contigs can also be provided to be used as long reads. SPAdes supports paired-end reads, mate-pairs and unpaired reads and can take as input several paired-end and mate-pair libraries simultaneously.
IMAGE / Iterative Mapping and Assembly for Gap Elimination
An approach to raise the quality of draft assemblies towards finished, but without manual intervention, using local assemblies of reads from gap regions. IMAGE utilises the large number of sequences that an Illumina Genome Analyzer produces. Reads that correspond to gaps or questionable regions are identified and reassembled locally before being incorporated back into the final assembly. An advantage of a local assembly as opposed to a de novo one is that the number of reads used is only a fraction of total available reads. This reduces the complexity of regions to be assembled as well as the time and computing memory required.
PAGIT / Post-Assembly Genome-Improvement Toolkit
Provides a toolkit for improving the quality of genome assemblies created via an assembly software. PAGIT compiled four tools: (i) ABACAS which classifies and orientates contigs and estimates the sizes of gaps between them; (ii) IMAGE uses paired-end reads to extend contigs and close gaps within the scaffolds; (iii) ICORN for identifying and correcting small errors in consensus sequences and; (iv) RATT for help annotation. The software was mainly created to analyze parasite genomes of up to about 300 Mb.
GapBlaster
A graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. GapBlaster uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps.
FinIS
Allows users to close gaps in the genome assembly as well as validate the genomic scaffold. FinIS considers all gaps simultaneously to find gap sequences that best match the read data and to correctly resolve repeats. Based on results for several real and simulated datasets, we demonstrate that FinIS validates the correctness of a larger fraction of the assembly than existing ad hoc tools. Using a test for unique optimal solutions, we show that FinIS can improve on both precision and recall values for the correctness of assembled sequences, when compared to competing programs.
OMACC / Optical-Map-Assisted Contig Connector
Obsolete
Closes the gaps between scaffolded contigs with a higher accuracy compared with a similar tool. OMACC is advantageous because it takes into account gap size carefully via rescaling optical map and applying length constraint on selecting the path of contigs for gap closure. In addition, it applies an advanced graph search algorithm to efficiently infer the correct number of repeat copies in the gap between two contigs. We apply OMACC and FINISH on both simulated and real data sets. OMACC achieves a >90% accuracy, higher than the <73% by FINISH, and more than doubles the contig N50 lengths. OMACC also maintains a similar sensitivity as FINISH does. Thus, OMACC should benefit various downstream biological studies via accurately connecting contigs into a more complete genome with the assistance of optical map.
G4ALL / Graphical contig analyzer for all sequencing platforms
Obsolete
A computational tool integrated with a database that allows the curation and extension of contigs produced by de novo assemblers, and the production of a scaffold, even when there is little overlap between the sequences (which can be validated by searching for homologies in biological databases). In addition, G4ALL allows various users to work on the project simultaneously, reducing the time needed for curation. G4ALL has a graphic edition and validation interface for de novo -assembled contigs, which allows the orientation and sorting of these contigs in relation to a reference genome based on the results of the alignment generated by the appropriate software in table format, with 11 columns (query, reference, alignment length, mismatches, gaps, query start, query end, source start, source end, evaluate, bitscore and identity). This software has been successfully used in a number of projects involving organisms such as Archaea and viruses.
FGAP
Obsolete
An efficient tool to find regions to fill gaps of draft genome sequences. FGAP demands low computational resources, the results can be easily analyzed by the output generated, and it can be used for small or large genome assemblies. FGAP can effectively reduce the effort to improve draft genome sequences in few steps, minimizing the number of unknown regions for human evaluation and reducing the need to obtain new data. In addition, FGAP has been successfully used to close gaps of draft sequences of several bacterial and fungal genome projects.
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