Description

Converts MAF alignments in another format.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

maf (file)

Multiple Aligment Format (MAF) file, optionally compressed with gzip

*.{maf.gz,maf}

format (string)

Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab)

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

versions (file)

File containing software versions

versions.yml

axt_gz (file)

Gzipped pairwise alignment in Axt (Blastz) format (optional)

*.axt.gz

blast_gz (file)

Gzipped pairwise alignment in blast format (optional)

*.blast.gz

blasttab_gz (file)

Gzipped pairwise alignment in blasttab format (optional)

*.blasttab.gz

chain_gz (file)

Gzipped pairwise alignment in UCSC chain format (optional)

*.chain.gz

gff_gz (file)

Gzipped pairwise alignment in GFF format (optional)

*.gff.gz

html_gz (file)

Gzipped pairwise alignment in HTML format (optional)

*.html.gz

psl_gz (file)

Gzipped pairwise alignment in PSL (BLAT) format (optional)

*.psl.gz

sam_gz (file)

Gzipped pairwise alignment in SAM format (optional)

*.sam.gz

tab_gz (file)

Gzipped pairwise alignment in TAB format (optional)

*.tab.gz

Tools

last
GPL v3-or-later

LAST finds & aligns related regions of sequences.