WhatsHap: fast and accurate read-based phasing
...al., Read-Based Phasing of Related Individuals). WhatsHap is easy to install It is easy to use: Pass in a VCF and one or more BAM files, get out a phased VCF. Suppor...2183 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad a...2151 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...abase genomes and deep-coverage sequencing. Quickly open and view data files on your computer without uplo...nd VCF data are displayed directly from chunks of the compressed binary files, no conversion needed. Inclu...2151 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...ools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer c...shared K-mers between two (or three) sequence files or hashes. sect: SEquence Co...s tools for filtering k-mer hashes and FastQ/A files: kmer: Produces a k-mer ha...1995 days ago
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Snippy: Rapid haploid variant calling and core SNP phylogeny
...many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can th...2039 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
...can be set by --long_read_batch_size N. Better compressed intermediate files. Added utilities folder. Added support for multiple short read files. Removed use of configuratio...2081 days ago
KAST: Perform Alignment-free k-tuple frequency comparisons from sequences
Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.2068 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entir...2053 days ago