benedictpaten/assemblaScripts benedictpaten/assemblaScripts

  • Stars
    star
    4
  • Rank 3,304,323 (Top 66 %)
  • Language
    C
  • License
    Other
  • Created over 13 years ago
  • Updated about 11 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
benedictpaten/assemblaScripts
github

benedictpaten

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Benchmarking scripts for assessing assemblies, used in the Assemblathon 1 project

More Repositories

1

intro_python

Lecture Notes and Slides for UCSC CSE20, formatted as Jupyter Notebooks.
Jupyter Notebook
78
star
2

marginPhase

C
34
star
3

sonLib

Small general purpose library for C and Python with focus on bioinformatics.
C
29
star
4

jobTree

Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)
Python
24
star
5

pinchesAndCacti

Library for constructing pinch graphs and cactus graphs
C
11
star
6

pecan

Probabilistic consistency based aligner
Java
8
star
7

cPecan

C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.
C
8
star
8

ortheus

Evolutionary transducer based method for aligning and reconstructing indel histories
C
6
star
9

assemblaLib

Library for Assemblathon 1 analysis scripts
C
3
star
10

cactusTools

A home for various common but non-essential scripts for the cactus project
C
3
star
11

pysqg

Prototype implementation of SQG parser in Python
Python
2
star
12

matchingAndOrdering

Library of matching and ordering algorithms, used for "reference problem"
C
2
star
13

Progressive-Alignment-with-Cactus

TeX
1
star
14

referenceScripts

Scripts for evaluating a cactus reference genome
C
1
star
15

progressiveBenchmarks

Evaluation scripts for testing cactus progressive method
Python
1
star