The phrase "assembly settings" is correct and usable in written English.
It can be used in contexts related to configuring or adjusting settings for an assembly process, such as in manufacturing or software development.
Example: "Before starting the production line, make sure to check the assembly settings to ensure everything is configured correctly."
Alternatives: "configuration settings" or "setup parameters".
[ 55], and assembled into contigs using default assembly settings of The Gene Indices Clustering Tools (TGICL), obtained from the Computational Biology and Functional Genomics Laboratory (The Gene Index Project, USA).
For MIRA assembly (settings: "--job=denovo,eSMARTrmadaptors), SMART adaptors were removed using BLAST and a custom perl script.
Draft RNA-seq assembly was performed with CLC Genomics Workbench v. 6.5 using standard de novo assembly settings.
Using less stringent CAP3 assembly settings, we identified 5951 contigs that were redundant and fully encompassed by other larger assemblies of sequences.
The length difference can be partially attributed to the relaxed comparative assembly settings that were used for Maq; no minimum read depth and mapping quality was used.
First MIRA3 [ 76] was used with the assembly settings of minimum sequence overlap of 30 bp and minimum percentage overlap identity of 80%.
Initial assemblies were used to find expected coverage and average sequenced fragment size, and a final optimized assembly with settings as described in the Materials and Methods section was performed, resulting in 1,305,238 contigs with a size of 100 bp or above, before the removal of contaminating sequence.
Raw reads were trimmed before de-novo transcript assembly with default settings at quality limit = 0.05, ambiguous limit = 2, and minimum number of nucleotides in reads = 15.
Shearing was performed using a Hydroshear® machine (GeneMachines®, San Carlos, CA) with a standard shearing assembly, using speed settings of 12 for the "circular" DNA sample and one aliquot of linearized DNA and 6 for another aliquot.
To initially identify the locations and DNA sequences of the NANOG gene and its pseudogenes in the chimpanzee genome, we used the GenBank entries for the human NANOG gene and its 11 pseudogenes as queries for MEGABLAST searches of the chimpanzee genome Build 1.1 assembly with default settings including filtering for repetitive sequences.
In other words, for each pepper line we obtained six Velvet assemblies (3 k-mers settings by 2 sets of reads) that were combined with CAP3 software yielding a super assembly.
