We used the above datasets to compare our Velvet-based pipeline with two other standalone assembly pipelines, SPAdes [ 11] and VICUNA [ 4].
Modular design is, for the most part, a method of designed a system as a series of almost-standalone assemblies or objects.
The manually assisted genome assembly procedure resulted in an order-of-magnitude decrease in the number of gaps in comparison to the Newbler assembler (which in turn performed the best out of all standalone assemblers evaluated).
ALLPATHS[ 9] is a standalone genome assembler.
One typically imports the model as a standalone item or an assembly using any of a number of acceptable formats, including STL.
Phrap is also widely used as a standalone tool for creating local assemblies of the BAC-sized (up to about 250K bases) regions of genomic sequence.
As a means for visualizing the spectral data, picked peaks and spin system assemblies underlying these assignments, we have developed the standalone software package described here, ADAPT-NMR Enhancer.
In order to examine the performance of two deterministic codes, nTRACER and the standalone developing version of the IDT solver of APOLLO3®, problems from 2D single assembly to 3D full core were computed with the same macroscopic cross-section library, so as to suppress the effects of physical modeling and to allow a direct comparison in terms of methodology, code architecture and performances.
We used the Eel Pond mRNAseq Protocol, a user-friendly standalone pipeline for complete transcriptome analysis from quality trimming and data normalization, through assembly, annotation, and expression analysis (https://khmer-protocols.readthedocs.org/).org/
To perform scaffolding with the BAC/fosmid ends, BLAST was used to map the paired reads to the assembly (≥95% identity, ≥ 100 bp alignment) to provide input to the standalone scaffolder, Bambus [ 12].
Standalone BLAST was used to obtain best matches for all unigene sequences derived after the CAP3 assembly program with a threshold E-value of ≤1E-05.
