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Javier Díez Pérez's starred repositories

favr

Filtering and Annotation of Variants that are Rare

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pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

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vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

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seqtk

Toolkit for processing sequences in FASTA/Q formats

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rq

Simple job queues for Python

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PyVCF

A Variant Call Format reader for Python.

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gemini

a lightweight db framework for exploring genetic variation.

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tutorial

The tutorial for xlrd, xlwt and xlutils

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pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

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Exo-Me

Collection of scripts that help categorize genetic finding in human disease

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EBCall

an empirical Bayesian framework for mutation detection from cancer genome sequencing data

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boto

For the latest version of boto, see https://github.com/boto/boto3 -- Python interface to Amazon Web Services

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bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

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qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

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qiime_test_data

Test input and output for QIIME scripts.

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Ion-Variant-Hunter

Variant Calling for Ion Torrent

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TMAP

Torrent Mapping Alignment Program

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seal

SEquence ALignment evaluation suite

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MOSAIK

reference-guided aligner for next-generation sequencing technologies

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pandoc

Universal markup converter

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bcbb

Useful bioinformatics code, primarily in Python and R

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biopython

Official git repository for Biopython (originally converted from CVS)

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bcbb

Incubator for useful bioinformatics code, primarily in Python and R

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