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awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

aws

Easy command line access to Amazon EC2, S3, SQS, ELB, and SDB (new!)

badread

a long read simulator that can imitate many types of read problems

bamtools

C++ API & command-line toolkit for working with BAM data

blasr

BLASR: The PacBio® long read aligner

blasr_libcpp

cligen

Nim library to infer and generate command-line-interfaces

daligner

Find all significant local alignments between reads

daligner-extras

Support for running DALIGNER (mostly scripts)

damasker

Module to determine where repeats are and make soft-masks of said

dascrubber

Alignment-based Scrubbing pipeline

datrie

Fast, efficiently stored Trie for Python. Uses libdatrie.

dazz_db

The Dazzler Data Base

dextractor

Bax File Decoder and Data Compressor

edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

falcon

FALCON: experimental PacBio diploid assembler

falcon-data

Very temporary storage for largish datafiles

falcon-examples

Examples on branches, and a useful place for testing

falcon-integrate

Build and integration- testing for FALCON

falcon-make

This is one way to install the FALCON packages residing in FALCON-integrate:

falcon-modules

DEPRECATED! Switch to FALCON-integrate

falcon-pbsmrtpipe

run.py etc using pbsmrtpipe instead of pypeFLOW

falcon-phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds

falcon-test

falcon3

falcon in python3

falcon_unzip

foo

falcon_unzip3

falcon-unzip in python3

fork

Subset of pitchfork

genomeworks

SDK for GPU accelerated genome assembly and analysis

gin

Gin is a HTTP web framework written in Go (Golang). It features a Martini-like API with much better performance -- up to 40 times faster. If you need smashing performance, get yourself some Gin.