“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...ransposon Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics for each TE family (number of TE copies, genome coverage...2176 days ago
2166 days ago
Digest: In silico restriction digest of complete genomes
This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragments is bellow 50, Pu...2197 days ago
2196 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...r easy plotting. gcp: K-mer GC Processor. Creates a matrix of the number of K-mers found given a GC co...he plot shows the amount of distinct K-mers absent, as well as the copy number variation present within the...1996 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...LAST-based ANI solver and it achieves two to three orders of magnitude speedup. Therefore, it is useful for pairwise ANI computation of large number of genome pairs. More details...2137 days ago
2112 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),...th standard somatic variant detection and copy number pipelines, and has support fo...ang D, Morrissey M (2016). “PureCN: Copy number calling and SNV classificatio...2110 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are diffic...2099 days ago
SimLoRD: A read simulator for third generation sequencing reads
...t file with integers (RNA), or using a fixed length Quality values and number of passes depend on fragment...length. Provided subread error probabilities are modified according to number of passes Outputs reads in F...2097 days ago