REFRESH Bioinformatics Group

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1. KMC KMC Public

   Fast and frugal disk based k-mer counter: counts 55-mers in 36 gzipped FASTQ files totaling 614 GB (WGS paired-end reads of NA12878, Illumina HiSeq 2000) in under 1.5 h, using 12 threads, 32 GB of …

   C++ 341 85

2. FAMSA FAMSA Public

   Algorithm for ultra-scale multiple protein sequence alignments: 3 million ABC transporters analyzed in 5 minutes and 18 GB of RAM.

   C++ 273 35

3. colord colord Public

   A versatile compressor of third generation sequencing reads.

   C++ 53 15

4. kmer-db kmer-db Public

   Fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, comparison): 16 million viral contigs analyzed in less than an hour.

   C++ 102 18

5. agc agc Public

   Assembled Genomes Compressor (AGC) squeezing 290 GB of Human Pangenome Project assemblies down to <1.5 GB (>190× ratio), with sample and contig extraction in seconds.

   C++ 187 20

6. vclust vclust Public

   Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

   Python 111 5