CBS-miRSeq

 Availability and requirements to use of CBS-miRSeq pipeline

 

Project name: CBS-miRSeq: a robust comprehensive bioinformatics pipeline for microRNA expression profiling by next generation sequencing.

Developer: Rupesh Kumar Kesharwani

Download link:

Source code:                   https://drive.google.com/file/d/0ByG63sGTZ4JTU2IzSjJVSjY1aXc/view?usp=sharing

User manual:                  https://drive.google.com/file/d/0ByG63sGTZ4JTaVRiVDNIWGJFOEE/view?usp=sharing

Test data:                        https://drive.google.com/file/d/0ByG63sGTZ4JTMnRxUVJPRWRoMjA/view?usp=sharing

Virtual Machine:          https://drive.google.com/file/d/0ByG63sGTZ4JTMVhrRGhnTDZzWGM/view?usp=sharing

Operating system(s): Linux/Unix.

Programming language: Bash, Perl and R.

Other requirements: Fastx(v0.0.14), FastQC (v0.10.1), SOLiD_preprocess_filter_v2.pl, cutadapt (v1.6), Bowtie (≤ v1.0), featureCounts (v1.4.6), samtools (v0.1.18), bedtools (v2.23.0), miRspring (v1.2),  miRDeep2 (v2.0.05), RNAhybrid (v2.1.1), miRanda (v3.3a), bioconductor packages (> v3), bfast (v0.6.5a).

License: GNU GPLv2.

Any restriction to use by non-academics: None

Contact information: In case of any query or feedback, feel free to contact Dr. Rupesh K. Kesharwani (rkesharwani@ccfm.it) / bioinforupesh2009.au@gmail.com