Genome assembly forensics: finding the elusive mis-assembly
...sp;amosvalidate. We demonstrate the application of our pipeline in both bacterial and eukaryotic genome assemblies, and highlight several assembly errors in both draft and finished ge...1954 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
HipSTR was specifically developed to deal with these errors in the hopes of obtaining more robust STR genotypes. In particular, it accomplishes this by: Learning locus-specifi...1914 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...alope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplex...1774 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
...; they are essentially made of stitched-together pieces of long reads. Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well...1644 days ago
NextDenovo: string graph-based de novo assembler for TGS long reads
...xtDenovo contains two core modules: NextCorrect and NextGraph. NextCorrect can be used to correct TGS long reads with approximately 15% sequencing errors, and NextGraph can be used to...1611 days ago
1602 days ago
QuorUM: An Error Corrector for Illumina Reads
We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found th...1580 days ago
LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
...e variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g....1567 days ago
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of...1539 days ago
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
...squo;s internal score. Merfin increased the precision of genotyped calls in several benchmarks, improved consensus accuracy and reduced frameshift errors when applied to human and non...791 days ago