(Open Java Development Kit) is a free and open source implementation of the Java Platform, Standard Edition (Java SE).

(BLAST-Like Alignment Tool) a very fast sequence alignment tool similar to BLAST.

GNU datamash is a command-line program which performs basic numeric,textual and statistical operations on input textual data files.

A method and tool to control single-cell RNA-seq data quality.

the Amazon Web Services (AWS) SDK for Python, which allows Python developers to write software that makes use of Amazon services like S3 and EC2. Boto provides an easy to use, object-oriented API as well as low-level direct service access.

provides a toolkit for analyzing single cell gene expression experiments. Monocle was originally developed to analyze dynamic biological processes such as cell differentiation, although it also supports other experimental settings.

A quality assessment package for next-genomics sequencing data. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well.