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 …
Fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, comparison): 16 million viral contigs analyzed in less than an hour.
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.
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.
Genome Differential Compressor 2 (GDC2) for FASTA collections, achieving ~9,500× compression on 1000GP data at 200 MB/s, featuring 1 GB/s decompression and direct single-genome extraction.
Space-efficient MUlti-Genome Index (MuGI) for FASTA reference + VCF collections, squeezing 1,092 diploid human genomes (6.7 TB) into 6.5–32 GB RAM for microsecond exact and mismatch search.
GTShark: Fast VCF GenoType compressor with rapid decompression and reference-based compression for external samples, squeezing a human genome down to ~65 KB.
VCF file compressor reaching over 30-fold efficiency on massive genotype datasets, with processing speeds up to 100 MB/s and peak memory usage below 30 GB.
The tool for creating k-mers counts matrices of many samples and computing various k-mer based statistics without need of a reference genome. The matrix may be built in less than 2 hours using less than 20 GB of RAM for reads of raw size over 12 TB.
Illumina read substitution and indel error corrector. Processes human WGS 45x depth reads in about 4 hours, resulting in the reads quality similar to other top algorithms.
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