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sequence-alignment

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biopython / biopython

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Martinsos / edlib

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Add windows command line support to aligner

3
randrick
randrick commented Oct 4, 2017

You can get aligner to work on windows command line by inserting the following lines into aligner.ccp
after line 8: #include <queue>

#ifdef _WIN32
#include "getopt.h"
#endif

#include "edlib.h"

Then adding getopt.h file. The one I used is here: https://raw.githubusercontent.com/skandhurkat/Getopt-for-Visual-Studio/master/getopt.h although that's likely not the origin of the fi

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enhancement good first issue

CMU-SAFARI / SneakySnake

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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/1910.09020.

fpga gpu smith-waterman needleman-wunsch sequence-alignment long-reads minimap2 short-reads hardware-accelerator sequence-aligner edlib pre-alignment-filtering
  • Updated May 12, 2021
  • VHDL

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