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Javier Díez Pérez's starred repositories

pandoc

Universal markup converter

Language:HaskellNOASSERTION33070 514 7473

rq

Simple job queues for Python

Language:PythonNOASSERTION9612 207 1139

boto

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

Language:PythonNOASSERTION6489 279 1665

biopython

Official git repository for Biopython (originally converted from CVS)

Language:PythonNOASSERTION4222 168 1664

seqtk

Toolkit for processing sequences in FASTA/Q formats

Language:CMIT1336 62 170

vcflib

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

Language:C++MIT604 39 270

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

Language:Python597 59 79

PyVCF

A Variant Call Format reader for Python.

Language:PythonNOASSERTION396 31 204

gemini

a lightweight db framework for exploring genetic variation.

Language:PythonMIT316 44 568

tutorial

The tutorial for xlrd, xlwt and xlutils

Language:Python310 390

pybedtools

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

Language:PythonNOASSERTION294 16 288

qiime

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

Language:PythonGPL-2.0285 58 1386

bio-playground

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

Language:CMIT181 16 16

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.

Language:C++GPL-3.0162 53 85

MOSAIK

reference-guided aligner for next-generation sequencing technologies

Language:C++55 9 32

TMAP

Torrent Mapping Alignment Program

Language:CGPL-2.049 23 14

EBCall

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

Language:Perl31 7 3

seal

SEquence ALignment evaluation suite

Language:JavaGPL-3.011 40

Ion-Variant-Hunter

Variant Calling for Ion Torrent

Language:Common LispNOASSERTION9 24 1

favr

Filtering and Annotation of Variants that are Rare

Language:PythonNOASSERTION7 60

qiime_test_data

Test input and output for QIIME scripts.

Language:JavaScript400

Exo-Me

Collection of scripts that help categorize genetic finding in human disease

3 30

bcbb

Useful bioinformatics code, primarily in Python and R

Language:Python1 20