chain-format is an actively used text data format created in 2013. The chain format describes a pairwise alignment that allow gaps in both sequences simultaneously. Each set of chain alignments starts with a header line, contains one or more alignment data lines, and terminates with a blank line. The format is deliberately quite dense.

7Years Old ?Users ?Jobs
  • chain-format first appeared in 2013
  • Have a question about chain-format not answered here? Email me and let me know how I can help.

Example code from the web:

chain 4900 chrY 58368225 + 25985403 25985638 chr5 151006098 - 43257292 43257528 1
9       1       0
10      0       5
61      4       0
16      0       4
42      3       0
16      0       8
14      1       0
3       7       0
48
chain 4900 chrY 58368225 + 25985406 25985566 chr5 151006098 - 43549808 43549970 2
16      0       2
60      4       0
10      0       4
70

Last updated February 18th, 2020

Edit chain-format on GitHub