Pandora's Modules

'Pandora's Modules' is the place to start, if you want to shock someone with the speed, quality and reusability of your bioinformatics programs. This is a collection of some of the best modules released under MIT/BSD type license (no copy-left ones) available online. We added or are in the process of adding a few missing blocks here and there and released all of them under MIT license.

All codes are written in C, as we usually try to stay away from C++. Therefore, we are in the process of readopt some of the available modules.

1. Klib by Heng Li (attractivechaos)

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https://github.com/attractivechaos/klib

This module provides a number of C routines for speedy processing of nucleotide data. It also includes a number of useful data structures. The README file at the above link explains how to use them in the code.

2. Hashlib - various hash related functions

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i) Hash functions

	OneAtATime

	FNV

	SuperFastHash

	lookup3

	MurmurHash



ii) Bloom filter


iii) KM-sketch


iv) Perfect hash

3. HPClib

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i) pthreads code


ii) shared memory code


iii) compare-and-swap

iv) queues

v) client-server codes

4. minimizer

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5. alignment-related codes

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i) oND
ii) siren
iii) smem
iv) smith-waterman

6. assembly-related codes

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i) alex-bowe
ii) bcalm 
iii) rect-graph

7. bwt-related codes

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i) BWT construction

ii) BWT search

8. kmers

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9. Bit level operations

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