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The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers.

Searching

ESTmapper

High-throughput cDNA to whole genome alignments using a powerful k-mer based filter coupled with sim4db.

Snapper

High-throughput searching and alignment of short to medium length genomic DNA to a genome.

Aligning

A2Amapper, ATAC, Assembly To Assembly Comparison

Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).

Sim4db

Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.

Analyzing

sim4db files

The output of snapper, ESTmapper and sim4db is in the sim4db format. We provide many utilities for processing this format, including converting to GFF3.

LEAFF

LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.

Meryl

An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Downloading

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