HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
...entation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that col...2231 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about t...ith a TE user-defined library Allow for working with only a user-chosen set of TE families http://do...2204 days ago
EAGLER: a scaffolding tool for long reads.
EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the...2204 days ago
Many-to-many pairwise alignments of two sequence sets
needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch...2189 days ago
2216 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...Typically this is used to compare a jellyfish hash produced from a read set to a jellyfish hash produced...t within the assembly. spectra-hist: Creates a K-mer spectra plot for a set of K-mer histograms produced...2024 days ago
Merqury: reference-free quality and phasing assessment for genome assemblies
...available for the assembled individual. The k-mer spectrum of this read set can be used for independently...quality without the need of a high quality reference. Merqury provides a set of tools for this purpose. h...1471 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...cult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled...e researcher wishes to de novo assemble specific content and a set of semi-similar reference tar...2152 days ago
LSC :a long read error correction tool
...will help you integrate LSC into your transcriptomics analysis pipeline. Read the LSC_requirements for running LSC. Download and set-up the LSC package. Follow t...2145 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
...ou 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 then take a set of Snippy results using the s...2067 days ago