Brent Pedersen (brentp)

brentp

Geek Repo

Company:University of Utah

Location:Utrecht, The Netherlands

Twitter:@brent_p

Github PK Tool:Github PK Tool


Organizations
quinlan-lab

Brent Pedersen's repositories

gargs

better(?) xargs in go

Language:GoLicense:Apache-2.0Stargazers:130Issues:8Issues:11

pyfasta

fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

hts-python

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Language:PythonLicense:MITStargazers:49Issues:12Issues:3

align

sequence alignment. global, local, glocal.

indelope

find large indels (in the blind spot between GATK/freebayes and SV callers)

Language:NimLicense:MITStargazers:39Issues:9Issues:6

fastbit-python

pythonic access to fastbit

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python-giggle

python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.

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gobio

miscellaneous script-like stuff in go for bioinformatics

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excord

extract SV signal from a BAM

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clinical-components

Summarize the clinical (or lab) components and correlations of your dataset.

skidmarks

find runs (non-randomness) in sequences

Language:PythonLicense:MITStargazers:7Issues:3Issues:4

bcf

bcf parsing in golang

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gemini

a lightweight db framework for disease and population genetics.

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go-giggle

golang wrapper to giggle

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htsuse

some C stuff that uses htslib

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seqtk

Toolkit for processing sequences in FASTA/Q formats

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bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

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go-athenaeum

a collection of small golang libraries I use

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HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data

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mmslice

mmap file to array of integers in go

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aegea

Amazon Web Services Operator Interface

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chroma

Everything you want to do with colors, in nim.

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CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

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easyssh

Golang package for easy remote execution through SSH (Fork enables cross-compile)

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giggle

Interval data structure

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go-stree

A package for Go that can be used for range queries on large number of intervals

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golsh

Approximate Nearest Neighbors in Go

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gonum

Gonum is a set of numeric libraries for the Go programming language. It contains libraries for matrices, statistics, optimization, and more

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grabix

a wee tool for random access into BGZF files.

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lsh

Locality Sensitive Hashing for Go (Multi-probe LSH, LSH Forest, basic LSH)

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