4 This contains our LIMS system and a collections of utilities
5 to help manage curation and submission of data.
10 Over time there were several different attempts to capture
11 and store "fastq-like" data. HTS-Workflow has at one time or
12 another supported NCBI srf files, Illumina qseq files, and
15 Because all of the current submitting agencies want fastq files.
16 There are some utilities to convert whatever is stored in our sequence
17 archive to fastq files.
19 The current ENCODE submission script is encode_submission/encode3.py
20 and it has a --fastq option that given a mapping file will try to
21 go find all the flowcells and generate condor scripts using
22 the lower level conversion utilities
24 * htsworkflow/pipelines/desplit_fastq.py
25 * htsworkflow/pipelines/qseq2fastq.py
26 * htsworkflow/pipelines/srf2fastq.py
28 desplit_fastq converts a list of fastq files into a single fastq file.
29 qseq2fastq takes a collection of qseq files or a tar-file containing
30 qseq files and converts it into a fastq file. and srf2fastq converts
33 Note: srf2fastq depends on the stadenio tools.
35 The encode3.py --fastq mode reads a mapping file that contains
37 library_id destination_directory
39 encode3.py has a '--compression gzip' option for if you want the
40 resulting fastq file to be compressed as a gzip file.