Sunday, 13 August 2017

Meet Nephele: Harness the Power of the Cloud for Your Microbiome Data Analysis

Nephele is a project from the National Institutes of Health (NIH) that brings together microbiome data and analysis tools in a cloud computing environment. It aims to address a major challenge facing researchers today — namely, analyzing, transferring, and storing biomedical "big data" — through the use of cloud-based resources

 Why Use Nephele?

  • Liberating: Nephele enables you to break free from constraints imposed on high-throughput computational analysis
  • Simple: Nephele is designed to be a no-hassle, easy-to-use tool to support your research
  • Sophisticated: Nephele is the most intuitive, advanced and secure microbiome analysis platform designed by our experienced computational biologists and software development team to provide exceptional capability with little effort on your part
  • Fast: Nephele speeds up microbiome data analysis and paves the path to getting to your results
  • Economical: Nephele's on-demand, pay-as-you-go setup offers a cost-effective alternative to using of dedicated resources for your microbiome data analysis
Ready to get started? Visit and enter your email address. Check your inbox for a message with the subject "Your Nephele Promotional Codes."
Stay in touch! Email with your questions and feedback. You can also visit our Google+ community page to connect with other researchers in the microbiome community (


demo bam file Ion Torrent 314 chip of E. coli 400 bp run for download

BAM file of B22-730 (314v2 E. coli 400 bp run)
Ion Torrent PGM 314v2 run with a mode read length of 400bp and per-base raw read accuracy >99%.


Wednesday, 2 August 2017

Creating filtered fastq files of ONLY mapped reads from a BAM file

Filtering BAM files for mapped or unmapped reads

To get the unmapped reads from a bam file use :
samtools view -f 4 file.bam > unmapped.sam, the output will be in sam
to get the output in bam use : samtools view -b -f 4 file.bam > unmapped.bam
To get only the mapped reads use the parameter 'F', which works like -v of grep and skips the alignments for a specific flag.
samtools view -b -F 4 file.bam > mapped.bam

Source: Sukhdeep Singh

To do this as efficiently as possible, using BBTools: in=reads.sam out=mapped.fq mappedonly
Also, BBMap has a lot of options designed for filtering, so it can output in fastq format and separate mapped from unmapped reads, preventing the creation of intermediate sam files.  This approach also keeps pairs together, which is not very easy using samtools for filtering. ref=reference.fa in=reads.fq outm=mapped.fq outu=unmapped.fq
Source: Brian Bushnell

Datanami, Woe be me