nimnexus: command-line tools for processing ChIP-nexus data

• trim: Filter, trim and rename sequences in the fastq according to the used barcodes
• dedup: De-duplicate PCR duplicates from a sorted BAM file

Installation

Download the binary from releases wget https://github.com/Avsecz/nimnexus/blob/master/nimnexus?raw=true -O nimnexus && chmod u+x nimnexus

Put it into a folder specified in $PATH.

Commands

Trim

$ nimnexus trim --help
nimnexus version:0.1.0

Trim the fastq reads

    Usage: nimnexus trim [options] <barcode>

Arguments:

   <barcode>    Barcode sequences (comma-separated) that follow random barcode

Options:

  -t --trim <int>           Pre-trim all reads by this length before processing [default: 0]
  -k --keep <int>           Minimum number of bases required after barcode to keep read [default: 18]
  -r --randombarcode <int>  Number of bases at the start of each read used for random barcode [default: 5]

Example:
  zcat input.fastq.gz | nimnexus trim -t 1 CTGA,TGAC,GACT,ACTG | gzip -c > output.fastq.gz

  # Using pigz to (de-)compress in parallel
  pigz -cd input.fastq.gz | nimnexus trim -t 1 CTGA,TGAC,GACT,ACTG | pigz -c > output.fastq.gz

Example:

zcat tests/data/mesc_pbx_raw_sample.fastq.gz | ./nimnexus trim -t 1 CTGA,TGAC,GACT,ACTG  > /tmp/output.fastq

Dedup

$ nimnexus dedup --help
nimnexus version:0.1.0

Remove duplicate reads from the sorted bam file

    Usage: nimnexus dedup [options] <BAM>

Arguments:

   <BAM>    sorted BAM file

Options:

  -t --threads <int>       number of BAM decompression threads [default: 2]

Example:
  nimnexus dedup -t 10 file.bam | samtools view -b > file.dedup.bam

Note: nimnexus dup writes the output in the SAM format to stdout. Hence samtools view -b is used to convert SAM->BAM.

Credit

• the original script written in R was implemented by by Melanie Weilert and Jeff Johnston. Repository: mlweilert/chipnexus-processing-scripts. Matching scripts:
  • nimnexus trim <-> scripts/preprocess_fastq
  • nimnexus dedup <-> scripts/process_bam.r
• nim package template was taken from Brent Pedersen's bpbio nim package: https://github.com/brentp/bpbio