cmu-safari/sneakysnake

SneakySnake:snake: 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.

sneakysnake's Issues

Unequal sequence lengths?

I'm interested in trying out SneakySnake, but as far as I can tell, aligning sequences with unequal lengths is not directly supported in the main SneakySnake() function. Is this an inherent limitation of the algorithm, or is it something which could be added without much effort? Especially for long reads, it seems quite uncommon to need to align (or pre-filter) a set of sequences which are all exactly the same length.

List commands and expected outputs

Could you please list the commands you used for performance evaluation and expected results for each dataset available in your repository ?

I am not familiar with your domain, but the output at https://github.com/CMU-SAFARI/SneakySnake/tree/master/Snake-on-GPU is for 3000 not 30,000. Is that right ?

When "Number_of_warps_inside_each_block" is not equal to 32, should we expect the same output result ?

For the following error, can I generate an index file using the command "mrfast --index human_g1k_v37.fasta" ?

WARNING: ./human_g1k_v37.fasta.fai not found, the SAM file(s) will not have a header.
You can generate the .fai file using samtools. Please place it in the same directory with the index to enable SAM headers.
Reference genome index file read error.

Thanks

make: *** No targets specified and no makefile found.

Hello,
Many thanks for providing SneakySnake.
On a xUbuntu18.04 machine with a singe user called minknow I tried to follow your instruction for getting started.
I did run:
in my home directory
git clone https://github.com/CMU-SAFARI/SneakySnake
Cloning into 'SneakySnake'...
remote: Enumerating objects: 649, done.
remote: Counting objects: 100% (66/66), done.
remote: Compressing objects: 100% (41/41), done.
remote: Total 649 (delta 29), reused 56 (delta 23), pack-reused 583
Receiving objects: 100% (649/649), 20.87 MiB | 10.79 MiB/s, done.
Resolving deltas: 100% (268/268), done.
minknow@meqneuropat24:~$ cd SneakySnake && make

and obtained this error:
make: *** No targets specified and no makefile found. Stop.

Frankly speaking I am not sure where to get started fixing this.
Could you please guide me to a solution?

Many thanks.