fsaina/debruijnbloom

Space-efficient and exact de Bruijn graph representation based on a Bloom filter, FER, Bioinformatics project

debruijnbloom's Issues

Comparation tool

"i sad bi to trebalo uzet(tih 7000) i pomoću BLASTa ili nekog drugog alata vidit koliko se to poklapa s originalnin genomon od E-Coli" M. Vernier

Program has to be super simple to setup

When we wrap up the project we need to make sure the project has to be super easy to setup and run on a linux machine

De Brujin Graph traversal implementation

A znas sve ca triba Verni :)

Alogrithm space time plotting

Implement time and memory measurements that would (ideally) output after run in a file (and then later used for plotting the performances in documentation)

Add MIT license

Compare our implementation with publishers

Run time, memory, accuracy comparisons with http://minia.genouest.org/

Start writing documentation

Pismeni dio:
-- U pismenom dijelu je potrebno:
-- opisati zadani algoritam/problem
-- objasniti isti kroz korake na jednostavnom primjeru
-- prikazati rezultati testiranja (vrijeme izvođenja i količina zauzete memorije -ako nije drugačije navedeno)
-- napisati zaključak
-- obavezno navesti korištenu literaturu
-- koristiti standardni FER obrazac za seminare

Find a bloom filter implementation

Find a bloom filter implementation that can be used for paper implementation, reference the paper for required specification

Write comments for every function and class

"svaka funkcija i klasa moraju biti komentirani"

move 'jullyfish' executable to './bin/jellyfish' for consistency

Argument checking

Add checks if input file exists and is readable (also for other tmp files as well)

Create syntethic dataset

Generirati barem 10 različitih sintetskih testnih podataka s različitm duljinama znakova. Testni slučaji
moraju obuhvaćati različite duljine nizova (100 –1000000 znakova)

Find testing tool

We need tool that gives us success score for contigs we build.
Download E.Choli genome and try how it works using one of the reads that we have in ecoli.fasta file(score should be ~1).