Logbook | Python Package Wiki

Based on how often these packages appear together in public requirements.txt files on GitHub.

cutadapt	trim adapters from high-throughput sequencing reads
fadapa	FAstqc DAta PArser - A minimal parser to parse FastQC output data in Python
bcbreport	report templates for bcbio analysis.
bcbio-nextgen	Best-practice pipelines for fully automated high throughput sequencing analysis
cyvcf	A fast Python library for VCF files using Cython for speed.
chanjo	Coverage analysis tool for clinical sequencing
gffutils	Work with GFF and GTF files in a flexible database framework
ipython-cluster-helper	Simplify IPython cluster start up and use for multiple schedulers.
pythonpy	python -c, with tab completion and shorthand
bioblend	CloudMan and Galaxy API library
arvados-python-client	Arvados client library
pybedtools	Wrapper around BEDTools for bioinformatics work
cyvcf2	fast vcf parsing with cython + htslib
bioepic	Chip-Seq broad peak/domain finder.
PyVCF	Variant Call Format (VCF) parser for Python
pystruct	Structured Learning and Prediction in Python
edlib	Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.
compare-reads	cythonized function to compare reads by name
cyordereddict	Cython implementation of Python's collections.OrderedDict

`pip install Logbook==1.5.3`