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Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina) data.

Molecular markers are valuable tools for breeders to help accelerate crop improvement. High throughput sequencing technologies facilitate the discovery of large-scale variations such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). Sequencing of chickpea genome along with re-sequencing of several chickpea lines has enabled the discovery of 4.4 million variations including SNPs and InDels. Here we report a repository of 1.9 million variations (SNPs and InDels) anchored on eight pseudomolecules in a custom database, referred as CicArVarDB that can be accessed at http://cicarvardb.icrisat.org/. It includes an easy interface for users to select variations around specific regions associated with quantitative trait loci, with embedded webBLAST search and JBrowse visualisation. We hope that this database will be immensely useful for the chickpea research community for both advancing genetics research as well as breeding applications for crop improvement. Database URL: http://cicarvardb.icrisat.org., (© The Author(s) 2015. Published by Oxford University Press.)

Background: Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions. Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until recently, limited numbers of molecular markers were available in the case of chickpea for use in molecular breeding. However, the recent advances in genomics facilitated the development of large scale markers especially SSRs (simple sequence repeats), the markers of choice in any breeding program. Availability of genome sequence very recently opens new avenues for accelerating molecular breeding approaches for chickpea improvement., Description: In order to assist genetic studies and breeding applications, we have developed a user friendly relational database named the Chickpea Microsatellite Database (CicArMiSatDB http://cicarmisatdb.icrisat.org). This database provides detailed information on SSRs along with their features in the genome. SSRs have been classified and made accessible through an easy-to-use web interface., Conclusions: This database is expected to help chickpea community in particular and legume community in general, to select SSRs of particular type or from a specific region in the genome to advance both basic genomics research as well as applied aspects of crop improvement.

We present a case of a 32-year-old hypertensive and obese male who had bilateral obstructive uropathy, and who was diagnosed as having pelvic lipomatosis on the basis of clinicoradiological findings. Cystoscopy and biopsy revealed cystitis cystica. He was successfully managed with bilateral extravesical modified Lich-Gregoir ureteric reimplantation by intraperitoneal approach. At 5 months follow-up, the patient had normal serum creatinine and was clinically asymptomatic., (Copyright (c) 2010 S. Karger AG, Basel.)

Endoscopic management of urolithiasis is one of the commonest urological procedures today. Its safety and efficacy in the management of ureteral calculi have been proven. A stone granuloma is a rare cause of recurrent ureteral obstruction subsequent to ureteroscopic stone removal. After its initial description by Dretler and Young [J Urol 1993;150:1800-1802] there have been sporadic reports of stone granuloma and paraureteral calculi secondary to iatrogenic perforations of the ureter and subsequent ureteric strictures as the cause of recurrent ureteral obstruction. We report two cases of delayed stone granuloma following pneumatic lithotripsy during ureteroscopy., (Copyright 2002 S. Karger AG, Basel)

Nephrocutaneous fistulas are rare complications of blunt or penetrating renal trauma. The majority are managed conservatively, some may require percutaneous drainage or ureteral stenting and some require operative intervention. Diversion of the urine by a ureteral stent usually aids in the healing of the fistula. We present an unusual case of nephrocutaneous fistula following blunt renal trauma which persisted as long as a stent was in place but healed immediately after the stent was removed.