mm2-fasthttps://github.com/bwa-mem2/mm2-fastmm2-fast is an accelerated implementation of minimap2 on modern CPUs. mm2-fast accelerates all the three major modules of minimap2: (a) seeding, (b) chaining, and (c) pairwise alignment, achieving up to
1.8x speedup using AVX512 over minimap2. mm2-fast is a drop-in replacement of minimap2, providing the same functionality with the exact same output. In the current version, all the modules are optimized using AVX-512 and AVX2 vectorization. Detailed benchmark results are available in our publication in Nature Computational Science (
https://www.nature.com/articles/s43588-022-00201-8).
strobealign: A fast short-read aligner
https://github.com/ksahlin/StrobeAlignhttps://www.biorxiv.org/content/10.1101/2021.06.18.449070v4.fullOur benchmarks on the four additional genomes drosophila, maize, CHM13, and rye broadly show similar results to our experiments on hg38. That is, on most datasets with read lengths 150nt or longer, strobealign and BWA-MEM have substantially higher accuracy than the other aligners (Suppl. Fig. S12). For example, strobealign is slightly more accurate than BWA-MEM (about 0.05%) on drosophila and slightly less accurate (at most 0.11%) than BWA-MEM on the new human genome CHM13 (Suppl. Fig. S12C). In addition, Strobealign is consistently 7-9 times faster than BWA-MEM on the maize, CHM13, and rye genomes (Suppl. Fig. S13) and 4-5 times faster than BWA-MEM2 and uses 2-3 times less peak memory than BWA-MEM2 (Suppl. Fig. S14).
SNAP – Scalable Nucleotide Alignment Program
https://www.microsoft.com/en-us/research/project/snap/SNAP is a program that is part of a gene sequencing pipeline. It takes data from gene sequencing hardware that consists of short chunks of DNA (typically 70-300 base pairs long) called reads and determines where, how well and how unambiguously they match to a given reference genome. This is a computationally challenging problem because reference genomes are big (the human genome is over 3 billion base pairs long) and are often highly repetitive.
SNAP is from 2-5x faster than commonly used aligners like BWA-mem2 and Bowtie2, and 20x-nearly 30x faster than Novoalign. When used with Haplotype Caller from the Genome Analysis Toolkit, SNAP produces better concordance with known-truth sets than other aligners for most of the genome-in-a-bottle and Illumina Platinum genomes.
SNAP is also more full-featured than other aligners. In addition to taking FASTQ (unprocessed reads) as input, it also accepts SAM and BAM (aligned reads). Other aligners produce unsorted SAM (or in the case of Novoalign unsorted BAM) output, and require the use of other tools to compress, sort, mark duplicates and index the final output file. SNAP does all of these tasks in a single tool, and is usually more than 10x faster than the standard samtools/Picard pipeline.
Тема: FASTQ->BAM (Прочитано 6524 раз)