#single-cell #preprocessing #rna-seq

bin+lib seq_geom_parser

A small crate for parsing library geometry specifications for single-cell sequencing

6 releases

0.3.0 Apr 6, 2023
0.2.1 Mar 19, 2023
0.1.3 Mar 7, 2023
0.1.1 Feb 3, 2023

#472 in Science

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seq geom parser

This is a rust crate for parsing the sequence fragment geometry description language (FGDL). This language is used to characterize the "geometry" of different sequencing technologies, in terms of how different positions and patterns in the sequenced reads encode information about the origin of the fragment (e.g. cell barcodes and unique molecular identifiers).

More details about the FGDL and the formal specification of the language can be found here.


This is a crate for parsing and interpreting sequence fragment geometry specifications in the sequence fragment geometry description language (FGDL). The FGDL describes how sequenced fragments are laid out, and how different parts of the sequence correspond to technical tags or to biological sequence. It provides a standard and unified way to represent the sequence layouts used in many different sequencing protocols, and is currently developed with a focus on representing different single-cell sequencing chemistries.

This crate provides a library for parsing these descriptions, and a set of structures for representing them in memory, as well as some common traits for transforming and printing them.


~60K SLoC