CBS-miRSeq

 Availability and requirements to use of CBS-miRSeq pipeline

 

Project name: CBS-miRSeq: a comprehensive tool for accurate and extensive analyses of microRNA-sequencing data.


Developer: Dr. Rupesh Kumar Kesharwani


Affiliation: 1. Unit of Immunology and Functional Genomics, Centro Cardiologico Monzino IRCCS, Milan, Italy

2. Department of Electrical, Computer and Biomedical Engineering, Università degli Studi di Pavia, Italy


Supervisors: Dr. Gualtiero I. Colombo (gualtiero.colombo@ccfm.it) and Prof. Riccardo Bellazzi (riccardo.bellazzi@unipv.it)


Download links:


Source code:      https://drive.google.com/file/d/0ByG63sGTZ4JTWl8tdkdSMThZN0E/view?usp=sharing

User manual:      https://drive.google.com/file/d/0ByG63sGTZ4JTd04zRXgyem1Ddmc/view?usp=sharing

Test data:            https://drive.google.com/file/d/0ByG63sGTZ4JTUHkxQlJmanV3VW8/view?usp=sharing

              

VirtualMachine:  https://drive.google.com/file/d/0ByG63sGTZ4JTSEVOSlhOVlE1UGs/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 GPLv3.


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)

Requested  Citation: Kesharwani RK et al. (2017) CBS-miRSeq: a comprehensive tool for accurate and extensive analyses of microRNA-sequencing data. BMC Genomics.