From 7261f44a69ca24ff2bcf5ed30e9931f5ee0eb2a6 Mon Sep 17 00:00:00 2001 From: thegenemyers Date: Fri, 23 Sep 2016 16:50:58 +0200 Subject: [PATCH] Harmonize before pull --- .gitignore | 137 ------------------------------------------------------------- README.md | 31 ++++++++++---- README2.md | 19 +++++++++ 3 files changed, 43 insertions(+), 144 deletions(-) create mode 100644 README2.md diff --git a/.gitignore b/.gitignore index d939e2e..405016f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,140 +1,3 @@ -<<<<<<< HEAD -## My stuff (Gene Myers) -.gitignore -.DS_Store -AUXILIARY - -## Core latex/pdflatex auxiliary files: -*.aux -*.lof -*.log -*.lot -*.fls -*.out -*.toc - -## Intermediate documents: -*.dvi -*-converted-to.* -# these rules might exclude image files for figures etc. -# *.ps -# *.eps -# *.pdf - -## Bibliography auxiliary files (bibtex/biblatex/biber): -*.bbl -*.bcf -*.blg -*-blx.aux -*-blx.bib -*.brf -*.run.xml - -## Build tool auxiliary files: -*.fdb_latexmk -*.synctex -*.synctex.gz -*.synctex.gz(busy) -*.pdfsync - -## Auxiliary and intermediate files from other packages: - -# algorithms -*.alg -*.loa - -# achemso -acs-*.bib - -# amsthm -*.thm - -# beamer -*.nav -*.snm -*.vrb - -#(e)ledmac/(e)ledpar -*.end -*.[1-9] -*.[1-9][0-9] -*.[1-9][0-9][0-9] -*.[1-9]R -*.[1-9][0-9]R -*.[1-9][0-9][0-9]R -*.eledsec[1-9] -*.eledsec[1-9]R -*.eledsec[1-9][0-9] -*.eledsec[1-9][0-9]R -*.eledsec[1-9][0-9][0-9] -*.eledsec[1-9][0-9][0-9]R - -# glossaries -*.acn -*.acr -*.glg -*.glo -*.gls - -# gnuplottex -*-gnuplottex-* - -# hyperref -*.brf - -# knitr -*-concordance.tex -*.tikz -*-tikzDictionary - -# listings -*.lol - -# makeidx -*.idx -*.ilg -*.ind -*.ist - -# minitoc -*.maf -*.mtc -*.mtc0 - -# minted -_minted* -*.pyg - -# morewrites -*.mw - -# nomencl -*.nlo - -# sagetex -*.sagetex.sage -*.sagetex.py -*.sagetex.scmd - -# sympy -*.sout -*.sympy -sympy-plots-for-*.tex/ - -# todonotes -*.tdo - -# xindy -*.xdy - -# WinEdt -*.bak -*.sav - -# specific to this repo -*.ver -======= *.html ->>>>>>> GFA-spec/master *.pdf !index.html diff --git a/README.md b/README.md index bce1b9b..7c32ebf 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,26 @@ -# A proposal for GFA 2.0 +# Graphical Fragment Assembly (GFA) Format Specification -Jason Chin, Richard Durbin, and myself (Gene Myers) found ourselves together at a workshop -meeting in Dagstuhl Germany and hammered out an initial proposal for an assembly format. -We thought GFA was a good start and built our design around it. We now offer it up for -comment, criticism, and refinement with the hope that a penultimate version of it might -be accepted by the GFA community and gain further significant adoption. +We are developing [the specification of the Graphical Fragment Assembly (GFA) format](GFA-spec.md). Your contribution is welcome. Please open up issues or submit pull requests. + +The format was first suggested in a [blog post](http://lh3.github.io/2014/07/19/a-proposal-of-the-grapical-fragment-assembly-format/) by Heng Li (@lh3) and further developed in a [second post](http://lh3.github.io/2014/07/23/first-update-on-gfa/). + +# Implementations + ++ [ABySS](https://github.com/bcgsc/abyss) ++ [Bandage](https://rrwick.github.io/Bandage/) ++ [bfgraph](https://github.com/pmelsted/bfgraph) ++ [fermi mag2gfa](https://github.com/lh3/mag2gfa) ++ [gfakluge](https://github.com/edawson/gfakluge) ++ [gfatools](https://github.com/lh3/gfatools) ++ [jts/DALIGNER](https://github.com/jts/daligner) ++ [lmrodriguezr/gfa](https://github.com/lmrodriguezr/gfa) ++ [McCortex](https://github.com/mcveanlab/mccortex) ++ [miniasm](https://github.com/lh3/miniasm) ++ [RGFA](https://github.com/ggonnella/RGFA) ++ [vg](https://github.com/ekg/vg) ++ [TwoPaCo](https://github.com/medvedevgroup/TwoPaCo) + +# Resources + ++ [Examples](https://github.com/sjackman/assembly-graph) of sequence overlap graphs (assembly graphs) in a variety of formats -The white paper is [here](GFA2-spec.md) diff --git a/README2.md b/README2.md new file mode 100644 index 0000000..8ce4c83 --- /dev/null +++ b/README2.md @@ -0,0 +1,19 @@ +# A proposal for a comprehensive assembly format + +Jason Chin, Richard Durbin, and myself (Gene Myers) found ourselves together at a workshop +meeting in Dagstuhl Germany and hammered out an initial proposal for an assembly format. +We thought [GFA](https://github.com/pmelsted/GFA-spec) was a good start point and built a +more comprehensive +design around it. We are calling this preliminary version the "Dagstuhl Assembly Format" or +[DAS](DAS-spec.md) and offer it up here for comment, criticism, and suggestions with the hope that +eventually some version of it might find adoption. + +The reason that we want a standard is that we find that +in general, *different* development teams build assemblers, visualizers, and editors because +of the complexity and distinct nature of the three tasks. While these tools should certainly +use tailored encodings internally for efficiency, the nexus between the three efforts +would benefit from a standard encoding format that would make them all interoperable. + +![Fig. 1](READ.Fig1.png) + +The white paper is [here](DAS-spec.md)