Best Practices for Variant Calling with the GATK
...9/15 Indel realignment Mark Fleharty PDF Video 03/19/15 Base quality score recalibration David Ro...d joint genotyping Sheila Chandran PDF Video 03/19/15 Variant quality score recalibration Bertrand...1562 days ago
flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and er...1500 days ago
Filtlong: quality filtering tool for long reads
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read iden...1481 days ago
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merqury: Evaluate genome assemblies with k-mers
...ds available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a...1429 days ago
SEASTAR: Systematic Evaluation of Alternative STArt site in RNA
...NA-seq data. It assembles novel TSSs based only on RNA-Seq data and merges them with known TSSs from a public database. This package enables high-quality TSS identification that is co...1389 days ago
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
...d works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce primary/alternate assemblies of quality competitive with the best ass...1256 days ago
FastProNGS: fast preprocessing of next-generation sequencing reads
FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest.1254 days ago
GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.
...and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To dem...1212 days ago
Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under ...1206 days ago