0.8.1

fasten container

Main tool: fasten

Code repository: https://github.com/lskatz/fasten

Basic information on how to use this tool:

• executable: fasten* (executables are found in /usr/local/bin)
• help: --help
• version: NA
• description: |

  A powerful manipulation suite for interleaved fastq files. Executables can read/write to stdin and stdout, and they are compatible with the interleaved fastq format. This makes it much easier to perform streaming operations using unix pipes.

There are several commands associated with fasten:

script	Description
fasten_clean	Trims and cleans a fastq file.
fasten_convert	Converts between different sequence formats like fastq, sam, fasta.
fasten_straighten	Convert any fastq file to a standard four-line-per-entry format.
fasten_metrics	Prints basic read metrics.
fasten_pe	Determines paired-endedness based on read IDs.
fasten_randomize	Randomizes reads from input
fasten_combine	Combines identical reads and updates quality scores.
fasten_kmer	Kmer counting.
fasten_normalize	Normalize read depth by using kmer counting.
fasten_sample	Downsamples reads.
fasten_shuffle	Shuffles or deshuffles paired end reads.
fasten_validate	Validates your reads (deprecated in favor of fasten_inspect and fasten_repair
fasten_inspect	adds information to read IDs such as seqlength
fasten_repair	Repairs corrupted reads
fasten_quality_filter	Transforms nucleotides to "N" if the quality is low
fasten_trim	Blunt-end trims reads
fasten_replace	Find and replace using regex
fasten_mutate	introduce random mutations
fasten_regex	Filter for reads using regex
fasten_progress	Add progress to any place in the pipeline
fasten_sort	Sort fastq entries

Full documentation: https://github.com/lskatz/fasten

Example Usage

cat testdata/R1.fastq testdata/R2.fastq | fasten_shuffle | fasten_metrics > fasten_metrics.txt
zcat testdata/R1.fastq testdata/R2.fastq | fasten_shuffle | fasten_clean --paired-end --min-length 2 | gzip -c > cleaned.shuffled.fastq.gz