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debarcer / De-Barcoding and Error Correction
Facilitates the use of barcoded data generated by SiMSenSeq. Debarcer is a package for working with next-generation sequencing (NGS) data that contains molecular barcodes. It processes raw .fastq files containing SiMSen-seq barcoded adaptor regions using a combination of standard bioinformatic tools such as bwa, perl and R, as well as Bio-SamTools, to extract information from alignment files. Debarcer collects the read data for each amplicon and barcode (a ‘sequence family’), and then, based on the alignment extracted from the .bam file, each base is indexed by genomic position.
MAGERI / Molecular tAgged GEnome Re-sequencing pIpeline
Allows to obtain high-fidelity mutation profiles and call ultra-rare variants by handling caveats of Unique Molecular Identifier (UMI)-based analysis. MAGERI accounts for polymerase chain reaction (PCR) errors by using a variant quality scoring model. It can handle reads with high error load, indels and random offsets. The tool was able to detect circulating tumor DNA (ctDNA) in peripheral blood of cancer patients. It allows easy and efficient processing of high-throughput sequencing data generated.
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