positionDB
in- and out-of-core kmer counting and utilities
Install
- All systems
-
curl cmd.cat/positionDB.sh
- Debian
-
apt-get install meryl - Ubuntu
-
apt-get install meryl - Kali Linux
-
apt-get install meryl - Windows (WSL2)
-
sudo apt-get updatesudo apt-get install meryl - Raspbian
-
apt-get install meryl - Dockerfile
- dockerfile.run/positionDB
meryl
in- and out-of-core kmer counting and utilities
meryl computes the kmer content of genomic sequences. Kmer content is represented as a list of kmers and the number of times each occurs in the input sequences. The kmer can be restricted to only the forward kmer, only the reverse kmer, or the canonical kmer (lexicographically smaller of the forward and reverse kmer at each location). Meryl can report the histogram of counts, the list of kmers and their counts, or can perform mathematical and set operations on the processed data files. This package is part of the Kmer suite.
canu
single molecule sequence assembler for genomes
Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: * Detect overlaps in high-noise sequences using MHAP * Generate corrected sequence consensus * Trim corrected sequences * Assemble trimmed corrected sequences