Preprocesses high-throughput sequencing data efficiently. Flexbar demultiplexes barcoded runs and removes adapter sequences. Several adapter removal presets for Illumina libraries are included. Flexbar computes exact overlap alignments using Single Instruction Multiple Data (SIMD) and multicore parallelism. Moreover, trimming and filtering features are provided: filter reads with uncalled bases, trim bases on left or right end, trim based on quality values, trim homopolymers at read ends, trim reads to certain length from right, and filter short sequencing reads. This tool increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. 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.