nicolaprezza/test-bs-aligner

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Created almost 10 years ago
Updated over 9 years ago

nicolaprezza/test-bs-aligner

nicolaprezza

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shell scripts to generate a BS experiment dataset and test on it a BS aligner + methylation caller

r-index

An optimal space run-length Burrows-Wheeler transform full-text index

BWTIL

BWT Text Indexing Library: a set of tools to work with BWT-based text indexes

CTLSAT

CTL (Computation Tree Logic) SAT solver

Re-Pair

A space-efficient compressor based on the Re-Pair grammar

lz-rlbwt

Run-length compressed BWT with LZ77 sampled suffix array

progetto_PEL_22_23

Progetto Programmazione e Laboratorio 2022-2023

cw-dBg

Compressed weighted de Bruijn graph

ebwt2InDel

ebwt2InDel: find SNPs and InDels from the BWT of a fasta read set

bwt2lcp

Compute the LCP array from the BWT of a set of DNA strings.

ebwt2snp

Positional clustering of the extended Burrows-Wheeler transform

high-order-lz77

LZ77 with High-order compressed pointers

cvs-rk

Critical Variables Selection via Rabin-Karp hashing

rlbwt2lcp

Compute minimum LCP value for each BWT equal-letter run

resource_monitor

Monitor memory usage (start and max RSS) and running time of a Linux process

slz-rlbwt

Super light index for repetitive text collections combining a sparse RLBWT with a sparse LZ77 parse

FMI

A simple wrapper on SDSL's FM-index

rk-lce

RK-LCE: a in-place LCE data structure based on Mersenne prime numbers

bioinfo-tools

bash scripts to process fasta/vcf/.. files

get-git-revisions

Checks out the last n versions (commits) of a git repository and concatenates all .cpp and .hpp files in all downloaded versions in a single file. I use this script to generate repetitive datasets on which I test my compression algorithms.