Sequence Transposition

Desktop

Phone

ASequences tab
BTool switcher
CInput files
DRun button
EFile panel

Transpose locus alignments into per-sample sequence files. Locus alignments store one locus per file with a sequence for each sample. Transposing creates one file for each sample with a sequence for each locus, for example to build sample-level references for read mapping.

Steps

Select Sequences in the navigation bar A.
Open Transpose sequences from the tool list on wide windows, or select the tool name B at the top of the page to switch tools.
Add the input files C with Browse files, Browse folder, or Open archive. SEGUI searches a folder and its subfolders for files that match the tool's input format. See file input for mobile options.
Select the input format (optional) and the data type.
Select Browse under Select output directory to choose the output folder. On phones and tablets, enter a Directory name instead; SEGUI saves it in the app's own folder.
Turn on Set interleaved format to write interleaved FASTA (optional).
Select the run button D, labeled Transpose, to start the task.

Output

The app writes each sample to its own folder: <sample>/<sample>.fas. Each sequence is named after the locus it comes from, which is the input file name without its extension. Gaps (-) and missing data (?) are removed, so the output is always unaligned FASTA. Samples missing from a locus are skipped for that locus.