diff --git a/docs/webapps/README.md b/docs/webapps/README.md index 819e219..70beeb3 100644 --- a/docs/webapps/README.md +++ b/docs/webapps/README.md @@ -4,11 +4,40 @@ Tracy features a range of companion web applications hosted at [https://www.gear ## Teal -ToDo +[Teal](https://www.gear-genomics.com/teal/) is a simple viewer for Sanger chromatogram traces. +The input tab of Teal requires a chromatogram trace file in scf, abi, ab1 or ab format. +The `Launch Analysis` button kicks off tracy and the results are +visualized in a separate browser tab. At the top, Teal shows the trace +signal. The navigation buttons on the top left side can be used to move +the actual view and zoom in or out. The buttons on the top right side +highlight a base of choice. The chromatogram sequence is provided below +the trace signal. + +![Tracy output page](./img/tracy-output.png) ## Sage -ToDo +[Sage](https://www.gear-genomics.com/sage/) +aligns a Sanger chromatogram trace to a reference sequence. The +input tab of Sage requires a chromatogram trace file in scf, abi, ab1 or +ab format. Optionally, a left and right trimming size for this trace can +be specified. We recommend using Teal for estimating such trim sizes. +Sage also requires a reference sequence as input. This can be either a +wildtype chromatogram, a small sequence in FASTA format or a large +indexed reference genome. + +Once these input requirements have been +specified the `Launch Analysis` button kicks off tracy and the results are +visualized in a separate browser tab. At the top, Sage shows the gapped +trace signal with the gapped reference aligned below. Mismatches between +reference and trace are colored red to highlight them for easy +identification. Traces with secondary peaks are colored orange. The +navigation buttons on the top left side can be used to move the actual +view and zoom in or out. The buttons on the top right side highlight a +base of choice. The chromatogram sequence and the reference sequence are +provided below the trace signal. + +![Sage output page](./img/sage-output.png) ## Indigo @@ -16,7 +45,49 @@ ToDo ## Pearl -ToDo +[Pearl](https://www.gear-genomics.com/pearl/) +is a tool to patch a DNA references with several Sanger trace +files. It has two main applications: (Parts) of a reference sequence +(fasta file, \*.fa) can be sequenced and Pearl highlights the conflicts +and mismatches between reference and the trace files. If no reference is +provided, a consensus sequence is assembled and used instead. + +The input +tab of Perl requires several chromatogram trace files in scf, abi, ab1 +or ab format. Pearl may use an optional reference sequence in FASTA +format as input. The user may choose if secondary peaks should be +treated as conflicts. Once these input requirements have been specified +the `Launch Analysis` button kicks off tracy and the results are +visualized in a separate browser tab. + +In the results tab Pearl shows the color-coded consensus overview +sequence on top: + +- light green - consensus: all traces agree on same base +- red - mismatch: traces agree on different base then reference +- orange - conflict: conflict, some traces suggest other bases +- green - edited: the base was entered manually by the user +- grey - no information: only reference data available + +By design, Pearl focuses only on one location, the position given below +the overview. A position can be selected by clicking at a position in +the overview sequence, by changing the number in the position field or +by navigating the trace windows. + +The available traces at the given position can be reviewed by the user +and manually set with the `Set...` buttons to a certain base. The `Jump to next conflict` button moves the position to the next conflict. Below the +traces three sequences are given + +1. the user sequence including all manually edited bases +2. the reference as uploaded +3. the consensus calculated by Pearl + +Once all mismatches and conflicts are edited by the +user, the sequence can be exported as FASTA. The entire dataset +including the traces can be saved as a JSON file and uploaded in the +result section later using the buttons at the top of the result tab. + +![Pearl output page](./img/pearl-output.png) ## Sabre @@ -40,4 +111,34 @@ as well as the alignment) is shown on the right. ## Wily-DNA-Editor -ToDo +The Wily-DNA-Editor is a tool for plasmid assembly, reverse complementing +DNA, translating to protein code and calculating restriction digests maps. + +The screenshot below illustrates the basic DNA/RNA operations that Wily can +perform, such as reverse-complementing DNA, removing non-IUPAC letters and +changing upper to lower case and vice versa. + +![Wily main controls](./img/wily-main.jpg) + +Furthermore, you can find restriction sites, select them and highlight them +in the sequence. + +![Wily digest controls](./img/wily-digest.jpg) + +You can draw restriction maps with or without features for linear +and circular sequences. + +![Wily map controls](./img/wily-map.jpg) + +You can simulate gel band intensity or draw all bands black. + +![Wily gel controls](./img/wily-gel.jpg) + +Translate DNA in one, three or six frames. + +![Wily translate controls](./img/wily-translate.jpg) + +Last but not least, Wily let's you annotate regions in the DNA +using GenBank features. + +![Wily feature controls](./img/wily-features.jpg) diff --git a/docs/webapps/img/pearl-output.png b/docs/webapps/img/pearl-output.png new file mode 100644 index 0000000..6c01c5f Binary files /dev/null and b/docs/webapps/img/pearl-output.png differ diff --git a/docs/webapps/img/sage-output.png b/docs/webapps/img/sage-output.png new file mode 100644 index 0000000..a281059 Binary files /dev/null and b/docs/webapps/img/sage-output.png differ diff --git a/docs/webapps/img/tracy-output.png b/docs/webapps/img/tracy-output.png new file mode 100644 index 0000000..0db3cc3 Binary files /dev/null and b/docs/webapps/img/tracy-output.png differ diff --git a/docs/webapps/img/wily-digest.jpg b/docs/webapps/img/wily-digest.jpg new file mode 100644 index 0000000..61d1632 Binary files /dev/null and b/docs/webapps/img/wily-digest.jpg differ diff --git a/docs/webapps/img/wily-features.jpg b/docs/webapps/img/wily-features.jpg new file mode 100644 index 0000000..7db307e Binary files /dev/null and b/docs/webapps/img/wily-features.jpg differ diff --git a/docs/webapps/img/wily-gel.jpg b/docs/webapps/img/wily-gel.jpg new file mode 100644 index 0000000..2bbc0d0 Binary files /dev/null and b/docs/webapps/img/wily-gel.jpg differ diff --git a/docs/webapps/img/wily-main.jpg b/docs/webapps/img/wily-main.jpg new file mode 100644 index 0000000..f1937ad Binary files /dev/null and b/docs/webapps/img/wily-main.jpg differ diff --git a/docs/webapps/img/wily-map.jpg b/docs/webapps/img/wily-map.jpg new file mode 100644 index 0000000..13026ed Binary files /dev/null and b/docs/webapps/img/wily-map.jpg differ diff --git a/docs/webapps/img/wily-translate.jpg b/docs/webapps/img/wily-translate.jpg new file mode 100644 index 0000000..608a82a Binary files /dev/null and b/docs/webapps/img/wily-translate.jpg differ