jstjohn/SimSeq

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Language
C
License
Other
Created about 14 years ago
Updated about 10 years ago

jstjohn/SimSeq

jstjohn

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An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.

SeqPrep

Tool for stripping adaptors and/or merging paired reads with overlap into single reads.

IntroToStatisticalLearningR-

Work on Introduction to Statistical Learning

KentLib

Subset of the kent source libraries (perhaps out of date) that are easily built and installed on OSX and Linux. These libraries provide usefull utilities for bioinformatics programming in C. This may contain some of my own libraries for bioinformatics utilities as well as long as they install easily on both my mac and linux box.

GrNMF

An R/Rcpp/RcppArmadillo implementation of Deng Cai's Non-negative Matrix Factorization on Manifold, sometimes called GNMF or GrNMF.

Jellyfish

Fork of the jellyfish kmer counter. Here is the description copied from their site: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish stats" command. See the documentation below for more details.

re-pair

Program to re-do the pairing of fastq reads. This program is modified from http://code.google.com/p/ngopt/source/browse/trunk/tools/pair_reads/repair.cpp?r=85

swift-c-htslib

Ultra-light HTSLIB wrapper for swift, currently just a modulemap giving you access to the C functions.

cscripts

Miscalanious C and C++ scripts.

swift-c-htslib-example

Example swift package built against CHTSLib

mia

MIA is an reference guided assembler for DNA reads as generated by recent sequencing technologies. It is designed to support unusual short reads like they come from ancient, fragmented DNA.

KinectOrbit

A fork of http://www.arduinoandkinectprojects.com/kinectorbit with an attempt at upgrading to Processing v2.

quora_querstion_pairs_kaggle

signalstepdetector

Automatically exported from code.google.com/p/signalstepdetector