isovic/graphmap-reproduce

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Python
License
MIT License
Created about 9 years ago
Updated over 8 years ago

isovic/graphmap-reproduce

isovic

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Scripts for testing and validating GraphMap.

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

raptor

Graph-based mapping of long sequences, noisy or HiFi.

wavelet-image-compression

Simple FPGA-based Wavelet Image Compression

aligned_vector

An STL-like std::vector implementation which internally aligns the array to a desired number of bytes. Intended for e.g. SIMD purposes.

minialign

Minimalistic aligner which uses Minimap for input mapping locations and Edlib for fast bitvector alignment.

cigargen

Simple DP implementation of Needleman-Wunsch for generating CIGAR strings for sequence alignments.

aracon

Assembly with RApid CONsensus from raw noisy long reads

consensus_from_mpileup

Scripts to compute simple consensus (SNPs, insertions, deletions) from mpileup by majority vote.

samscripts

seqlib

A codebase for sequence analysis projects. Highly experimental and in development.

argparser

Library for parsing command line arguments. Allows short and long arg names, specifying parameter groups and default values.

evalue

E-value calculation with predefined BLAST parameters.