Allows barcode and adapter detection. Flexbar calculates full overlap alignments using Single Instruction Multiple Data (SIMD) and multicore parallelism. It allows to filter reads with uncalled bases, trim bases on left or right end, detect barcode, remove and read separation, detect and remove adapter, trim reads to certain length from right and filter short sequencing reads. The performance of the software was evaluated by adapter trimming.
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.
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.