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milkweedgenome.org - Some of the useful bioinformatics scripts. For example ... contig-stats.pl is a Perl script that will automatically describe features of a sequence assembly. http://milkweedgenome.org/?q=scripts

readthedocs.org - Bipype is a very useful program, which prepare a lot of types of bioinformatics analyses. There are three input options: amplicons, WGS (whole genome sequences) and metatranscriptomic data. If amplicons are input data, then bipype does...

$ sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose[sudo] password for urbe: Reading package lists... DoneBuilding dependency tree Reading state information... DoneThe...

If you have a later version than 2.6 you'll need to set 2.6 as the default Python.

github.com - Nucleus is a library of Python and C++ code designed to make it easy to read, write and analyze data in common genomics file formats like SAM and VCF. In addition, Nucleus enables painless integration with the TensorFlow machine learning framework,...

Python projects

github.com - snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C Whole Genome Bisulfite Seq/WGBS (*Also available in...

github.com - There is a directory for each chapter of the book. Each directory contains a test.py program you can use with pytest to check that you have written the program correctly. I have included a short README to describe each exercise....

wgs-assembler.sourceforge.net - These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.This distribution package provides a stable, tested, documented version of the software.  The distribution is usable on most Unix-like platforms,...

telatin.github.io - A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and...