SHORE v0.7 file formats

Any output generated by SHORE will usually be written to various text files that contain a number of tab-delimited columns.

Typing shore fmt will display a quick reference for many of SHORE’s file formats.

This page only describes SHORE's read and alignment file formats; other files formats will be described on the page of the respective subprogram that generates them.

Read file format

Read files can be found in the LengthFolders or ReadFolders. These files are created by shore import and are named reads_0.fl.

reads_0.fl files are usually sorted on the id field in numerical order.

The tab delimited entries are:

id	A unique identifier for the read or read pair
sequence	DNA sequence
pe	Flag, ’1’ or ’2’, first read or second read of a read pair. ’0’ for a single-end read.
Sanger quality values	String of sanger calibrated quality values Encoding: ASCII 33 ('!', quality 0) to ASCII 73 ('I', quality 40); extended range ASCII 93 (']', quality 60)
[Chastity values] (Optional column)	String of illumina chastity values (defined as <math>Intensity(max)/ (Intensity(max) + Intensity(second))</math>). Encoding: ASCII 40 ('(', chastity of 0.5) to ASCII 90 ('Z', chastity of 1.0)

Note: Earlier versions of SHORE used a read file format featuring three different quality types per entry. This file format is still supported for reading, but is no longer written.

Alignment file format

SHORE alignment files are typically named map.list, map.list.1 or map.list.2. They are stored in the LengthFolders or ReadFolders.

map.list files are sorted in numerical order, either on the fields chr id and pos, or on the field read id.

The tab delimited entries are:

chr id	Each chromosome has an internal id, simply enumerated according to their occurrence within the reference sequence file, starting from 1. Translation to the native chromosome name can be found in the *.shore.ref and *.shore.trans file in the IndexFolder, or in the ref.txt files created by shore mapflowcell.
pos	Left-most position of the alignment relative to the forward strand of the reference sequence. The first position of a chromosome is 1.
alignment	String representation of the read alignment. The sequence is always reported with respect to the forward strand of the reference, i.e. the sequence of reads matching to the reverse strand is reverse complemented. Matches are reported as a single IUPAC character Mismatches or gaps as two characters surrounded by brackets. The first character represents the reference base, the second character the sequenced base. Deleted nucleotides are represented as ’-’. Examples: [CT] (mismatch), [-T] (insertion), [C-] (deletion) Long deletions with respect to the reference may be reported as the character L followed by the size of the deletion, e.g. [L100] Unaligned sequence ('soft clip') may be reported in angle brackets, e.g. <TTTTTT> Extensions, not supported by all tools: Consecutive stretches of the same operation (mismatch, insertion, deletion) may be abbreviated, e.g. [CTT|---] instead of [C-][T-][T-] F can be used to indicate a mapped part of a fragment with known size, but unknown sequence, e.g. [F100]
read id	A unique identifier for the read or read pair
strand	D for forward and P for reverse hits (direct and palindromic, respectively).
mismatches	The number of mismatches+gaps in the alignment.
hits	The total number of genomic positions the read is aligned to.
read length	Length of the read ('soft clipped' nucleotides excluded).
offset	Alignment start offset into the read (local alignments, first base of the read is 1) 0: no offset, the read/query is fully aligned (soft clip is still possible) ≥1: The read/query is only locally aligned and the alignment starts at the specified position. Unaligned portions are not represented in the alignment string.
pe flag	Paired-end information 0: single read 1: first read of a pair (state of read 2 is either filtered or has not been assessed yet) 2: second read of a pair (state of read 1 is either filtered or has not been assessed yet) 3: first read of a pair (concordant mapping: distance of read 2 is in the range of the insert size distribution) 4: first read of a pair (discordant mapping: distance of read 2 is not in the range of the insert size distribution) 5: first read of a pair (orphan read: read 2 is unmapped) 6: second read of a pair (concordant mapping: distance of read 1 is in the range of the insert size distribution) 7: second read of a pair (discordant mapping: distance of read 1 is not in the range of the insert size distribution) 8: second read of a pair (orphan read: read 1 is unmapped) A library ID <math>L</math> may be encoded in the pe flag for the flags with value <math>>2</math>; in this case the flag is calculated as <math>pe\_flag = pe\_flag + (L * 6)</math>
Sanger quality values	String of sanger calibrated quality values. Encoding: ASCII 33 ('!', quality 0) to ASCII 73 ('I', quality 40); extended range ASCII 93 (']', quality 60)
[Chastity values] (Optional column)	String of illumina chastity values defined as the highest intensity divided by the sum of the highest and the second highest intensity of a single base. Encoding: ASCII 40 ('(', chastity of 0.5) to ASCII 90 ('Z', chastity of 1.0)

Note: Earlier versions of SHORE used an alignment file format featuring three different quality types per entry. This file format is still supported for reading, but is no longer written.