Crate fasten

Perform random operations on fastq files, using unix streaming. Secure your analysis with Fasten!

Synopsis

read metrics

 
$ cat testdata/R1.fastq testdata/R2.fastq | \
    fasten_shuffle | fasten_metrics | column -t
totalLength  numReads  avgReadLength  avgQual
800          8         100            19.53875

read cleaning

$ cat testdata/R1.fastq testdata/R2.fastq | \
    fasten_shuffle | \
    fasten_clean --paired-end --min-length 2 | \
    gzip -c > cleaned.shuffled.fastq.gz
 
$ zcat cleaned.shuffled.fastq.gz | fasten_metrics | column -t
totalLength  numReads  avgReadLength  avgQual
800          8         100            19.53875

NOTE: No reads were actually filtered with cleaning, with –min-length=2

Kmer counting

$ cat testdata/R1.fastq | \
  fasten_kmer -k 21 > 21mers.tsv

Read sampling

$ cat testdata/R1.fastq testdata/R2.fastq | \
    fasten_shuffle | \
    fasten_sample --paired-end --frequency 0.1 > 10percent.fastq

Advanced

Set of downsampled reads

Create a set of downsampled reads for a titration experiment and clean them

for frequency in 0.1 0.2 0.3 0.4 0.5; do
  cat testdata/R1.fastq testdata/R2.fastq | \
    fasten_shuffle | \
    fasten_clean --paired-end --min-length 50 --min-trim-quality 25
    fasten_sample --paired-end --frequency $frequency > cleaned.$frequency.fastq
done

Validate a whole directory of fastq reads

\ls *_1.fastq.gz | xargs -n 1 -P 4 bash -c '
  echo -n "." >&2 # progress bar
  R1=$0
  R2=${0/_1.fastq.gz/_2.fastq.gz}
  zcat $R1 $R2 | fasten_shuffle | fasten_validate --paired-end
'

Modules

io

input/output methods

Macros

print

Rewrite print!() so that it doesn’t panic on broken pipe.

Functions

eexit

Propagate an error by printing invalid read(s)

fasten_base_options

a function that reads an options object and adds fasten default options.

logmsg

Print a formatted message to stderr