The phrase "a reference assembly against" is correct and usable in written English.
It can be used in contexts where you are discussing a standard or benchmark to compare or evaluate something.
Example: "The researchers created a reference assembly against which all new samples could be measured for accuracy."
Alternatives: "a benchmark assembly for" or "a standard assembly to compare against".
A reference assembly against the 15.5 kb contig yielded 35,120 sequence reads with full coverage across the entire contig.
A reference assembly against this 15.2 kb contig yielded 1,068 sequence reads with full coverage across the entire contig.
The contaminating chloroplast sequence reads were removed by performing a reference assembly against the chloroplast genome (GenBank Acc. No.: NC_009950.1).
The chloroplast reads were removed by performing a reference assembly against the perennial ryegrass chloroplast genome (GenBank Acc. No.: NC_009950.1) using the parameters: similarity, 0.98; conflict resolution, vote (A, C, G, T); non-specific matches, random and masking of references, none.
In order to confirm the validity of our sequences and to test the de novo assembly against a reference assembly, we also assembled the junco transcriptome using GMAP [ 38] with standard parameters against the closest available draft genome assembly: the zebra finch the first passerine genome sequencing project [ 39], and a species that diverged from juncos approximately 25 Ma ago [ 40].
Average coverage of the assembled data was identified by performing a reference assembly of the sequencing data against the assembled sequence using Newbler (454/Roche).
To align the sequenced data against a reference assembly, GensearchNGS provides the user with many options.
Therefore a correction was carried out by performing a reference assembly of the short reads from the Illumina sequencing against the reclosed genome, yielding the final genome sequence.
A further analysis of the reference assembly against a linearized 630 genome revealed four breakpoints (regions with discordantly mapped read-pairs).
Preliminary analysis indicated good coverage of the polymerase region of the ARCoV.2 reference sequence by the reads (quality index >40) by using reference assembly against CoV complete genomes.
