brainstorm

input {
  file {
    type => "rodslog"
    start_position => beginning
    debug => true
    sincedb_path => "/root/logstash/.sincedb"
    path => [ "/root/logstash/logs/eu/var/log/irods/rodsLog.*" ]
  }
}

nathanhaigh

#!/bin/bash
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
# 
# Deinterleaves a FASTQ file of paired reads into two FASTQ
# files specified on the command line. Optionally GZip compresses the output
# FASTQ files using pigz if the 3rd command line argument is the word "compress"
# 
# Can deinterleave 100 million paired reads (200 million total
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
# 

brantfaircloth

Install dependencies and Casava

The following assumes you are converting BCL files containing PE100 reads with a 10 nt index read. You can allow Casava to demultiplex for you or do it on your own, later. You can adjust values below if you are doing something different (e.g. shorter reads, longer indexes) but be careful.

• You need a pretty beefy machine. Illumina recommends something with multiple cores and 48 GB RAM, running Centos 5. Centos 6 also works just fine. See their recommendations here: