Seal Utilities

We’ve included in the bin directory of the Seal distribution some of the utilities and scripts we use internally. These may not be all maintained (it depends on whether we’re using them at the moment). Use at your own risk!!

Note that some of these utilities don’t follow the Seal usage convention.

distcp_files

A utility useful for uploading files to HDFS.

Under the hood, it uses hadoop distcp, but it avoids you having to prepend file:// to local files.

Usage:

bin/distcp_files filenames*  hdfs_dest_directory

tsvsort

A distributed sorting program for large text files. See the TsvSort page for details.

align_script

A script to perform read alignment using libbwa (the same one used by Seqal).

Usage:

bin/align_script [OPTIONS] --reference=REFERENCE PRQFILE PRQFILE

You can also pipe it input in prq format via stdin.

find_fq_format

Reads a fastq file and tries to determine whether the base qualities are encoded in Sanger or Illumina format.

prq_local

Reformat a pair of qseq files (one for reads 1, one for reads 2) into a prq file. Read mates have to appear on the same line of their respective files.

Usage:

bin/prq_local reads1.qseq reads2.qseq output.prq

prq_to_fastq

Split a prq file into two fastq files.

Usage:

bin/prq_to_fastq input.prq reads1.fastq reads2.fastq

realign_snp

Realign SNPs. See the documentation in the script file for details.