2218 days ago
2218 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
...rated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human refe...2218 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
...y aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure...2216 days ago
2213 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...ents. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance. Can...2181 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...the "comp" tool. Typically this is used to compare two K-mer hashes produced by different NGS reads. profile: Creates a K-mer coverage plot for a single sequence. Takes in fasta cove...2026 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designe...2140 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
...ns/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores)...with speed in mind, and produces a consistent set of output files in a single folder. It can then take a se...2069 days ago
2127 days ago