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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