further use with short read length. This distribution-shifting approach was chosen to achieve a realistic distribution of read length rather than trimming all reads by fixed lengths. These datasets were labeled as 16k and 11k based on their N50 of subread data of 16,765, and 11,092, ...
XICRA uses cutadapt [30] for the adapter trimming analysis. Default trimming preset parameter settings are: to keep all reads regardless of whether the adapter is found or not, a 10% maximum adapter matching error rate (mismatches, insertions and deletions), and a 3 bp minimum overlap length....
Adaptor sequences removal and trimming was performed using BBDUK (BBtools suite) with the following settings: ordered = t; ktrim = r; k = 23; mink = 11; hdist = 1; qtrim = rl; trimq = 20; min.length = 35; tpe; tbo. A further rRNA contamination step was conducted using BBDUK ...
Genome sequencing data resulted in the presence of one contig, which demonstrated a length of 17,155 bp linear, double-stranded DNA. According to our TEM result, the phage belonged to the Rountreeviridae family, which is also confirmed by the genome annotation and using the blast tool against...
Sequence Length Distribution - Nothing to check here for raw Illumina reads - all reads are the same length. However, this plot could be useful for adapter- and quality- trimmed reads to see how long the remaining good quality reads are. ...
After digestion with RNase I, the cDNA/RNA hybrid was purified using the cap-trapping method, and full-length single-strand cDNAs were obtained. A 5′ adaptor (Additional file 6: Table S6) was attached to the cap-trapping single-strand cDNAs, and second-strand cDNAs were synthesized using ...
annotation. Sequence identity was calculated with ClustalW (v2.1), and TM scores were generated using TM-align (https://zhanggroup.org/TM-align/). TM score was normalized according to the length of the reference protein. Gold: Identified microsporidian proteins; magenta: Homologs; AF, AlphaFold...
-i- The input kreport file from kraken2, denoted for parallel by {1} because it's the first option outside of the quoted bracken command after the::: -r- The length of the reads used for mapping -l- The level at which to estimate taxon abundance (S indicates species), den...
4.2 for each dataset—Supplementary Information). Quality based trimming of these short-read datasets was performed at a stringent cut-off value of 0.02. More details about the trimming algorithm used by CLC and an example can be found in online documentation40. After quality trimming, only a ...
a Length distribution for 11,120 assembled contigs classified as CoV-positive, showing a peak around the typical CoV genome length, 4,179 (37.58%) of contigs also contained a match for RdRP. b Phylogram shown in Figure 3 showing the Mesoniviridae, Tobaniviridae, and Roniviridae outgroups. ...