Software
SAUTE- New assembler for sequence assembly using target enrichment
- /var/www/html/wp-content/plugins/mvp-social-buttons/mvp-social-buttons.php on line 27
https://bioinformaticsreview.com/wp-content/uploads/2021/07/saute.jpg&description=SAUTE- New assembler for sequence assembly using target enrichment', 'pinterestShare', 'width=750,height=350'); return false;" title="Pin This Post">
- Share
- Tweet /var/www/html/wp-content/plugins/mvp-social-buttons/mvp-social-buttons.php on line 69
https://bioinformaticsreview.com/wp-content/uploads/2021/07/saute.jpg&description=SAUTE- New assembler for sequence assembly using target enrichment', 'pinterestShare', 'width=750,height=350'); return false;" title="Pin This Post">
A new assembler called SAUTE is developed for sequence assembly that is based on target enrichment [1].
SAUTE stands for sequence assembly for target enrichment. It efficiently assembles repeat regions and reports multiple well-supported variants. Users can provide target sequences for assembly assistance. The authors have developed two assemblers namely, SAUTE and SAUTE_PROT.
How SAUTE works?
At first, SAUTE reads input files in fast or fastq or SRA format and trim reads. After that, it builds two De Bruijn Graphs followed by finding and assembling subgraphs. These subgraphs are further filtered using the alignment of reads and read pairs to the assembled graph. Further, it assembles additional sequences beyond the ends if a user opts to do so. Finally, it reports output in the format of graphical fragment assembly along with two fasta files.
As compared to TRINITY, RNASPADES, SPALIGNER, and SPADES in the case of RNA-seq, SAUTE_PROT outputs more coding sequences translating to benchmark proteins.
SAUTE is currently available for Linux only. It is available to download on GitHub.
For more information, read here.
References
- Souvorov, A., Agarwala, R. (2021). SAUTE: sequence assembly using target enrichment. BMC Bioinformatics 22, 375.
Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)
Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].
AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)
Warning: Undefined variable $user_ID in /var/www/html/wp-content/themes/zox-news/comments.php on line 49
You must be logged in to post a comment Login