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Top 3 short-reads open source projects

TypeTE

Genotyping of segregating mobile elements insertions

✭ 15

perl python shell bioinformatics vcf alu transposons transposable-elements genotype-likelihoods genotyping short-reads

SSAKE

🍶Genome assembly with short sequence reads

✭ 20

perl python shell dna-sequences genome-scaffolding short-reads sequence-assembly genome-assembler read-pairs

SneakySnake

SneakySnake🐍 is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs…

✭ 44

VHDL Verilog shell C++Cuda SystemVerilog fpga gpu smith-waterman needleman-wunsch sequence-alignment long-reads minimap2 short-reads hardware-accelerator sequence-aligner edlib pre-alignment-filtering wavefront-alignment

1-3 of 3 short-reads projects