sumQC
sumQC is a bioinformatics pipeline for cleaning 2nd and 3rd generation sequencing data. In addition, the program also gives the user a summary table of the sequence data quality before and after the cleaning in the tab-delimited text format, ready to be used for publication. The pipeline is written using the bioinformatics workflow manager Nextflow, a powerful and flexible workflow language that allows multiple tasks at different processing levels to be run parallelly.
snpplet processes short-read sequencing data to obtain short variants (SNPs and indels). It implements tools for raw read data quality control and preprocessing, read mapping, variant calling, and filtering to produce an analysis-ready vcf file. snpplet incorporates workflows from samtools and the GATK Best Practices for germline short variant discovery. It also includes a step to parse the SNV table into a multiple sequence alignment (MSA) in the FASTA format.
snpplet
Entourage
Virus identification is a common task in today’s virological and clinical research. Entourage identifies viruses in your samples by using de novo assembly, allowing for the discovery of uncommon/novel viruses, and giving you their genome sequences at the same time. Entourage can also provide intra-sample nucleotide variations, useful for analysis of mutation dynamics, or the presence of coinfection, for example.
Asanovi is a bioinformatics pipeline for bacterial de novo genome assembly. The pipeline accepts both 2nd and 3rd-generation sequencing reads as input. In addition to assembling the reads, the pipeline also evaluates the quality of the assembly results and summarises them in a single HTML report.
Asanovi
Pornchai Matangkasombut Center for Microbial Genomics
Department of Microbiology, Faculty of Science, Mahidol University
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