Andreas Tille pushed to branch upstream at Debian Med / dnarrange
Commits: 978a034b by Andreas Tille at 2022-07-19T11:58:56+02:00 New upstream version 1.5.3 - - - - - 2 changed files: - README.md - setup.py Changes: ===================================== README.md ===================================== @@ -109,12 +109,12 @@ and [MAFFT][] to be installed). Then re-[align](https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md) -the merged reads to the genome (it's recommended to do this without -repeat-masking): +the merged reads to the genome (maybe using e.g. `-m20` or `-m50` to +make it more sensitive-but-slow): lastdb -P8 -uNEAR mydb genome.fa last-train -P8 mydb merged.fa > merged.par - lastal -P8 -p merged.par mydb merged.fa | last-split > merged.maf + lastal -P8 -m20 --split -p merged.par mydb merged.fa > merged.maf And draw pictures: @@ -266,7 +266,7 @@ You can get the rearranged reads, without merging them, like this: dnarrange-merge all-reads.fq groups.maf > some-reads.fq This may be useful if you wish to re-align the rearranged reads to the -genome more slowly-and-carefully (e.g. without repeat-masking). +genome more slowly-and-carefully. `dnarrange-merge` also has options that it passes to `lamassemble`: you can see them with `dnarrange-merge --help`, and they're described ===================================== setup.py ===================================== @@ -1,6 +1,6 @@ import setuptools -commitInfo = " (HEAD -> master, tag: 1.5.2)".strip("( )").split() +commitInfo = " (HEAD -> master, tag: 1.5.3)".strip("( )").split() version = commitInfo[commitInfo.index("tag:") + 1].rstrip(",") setuptools.setup( View it on GitLab: https://salsa.debian.org/med-team/dnarrange/-/commit/978a034b2890501a402d6e222b5dc5ba9b645727 -- View it on GitLab: https://salsa.debian.org/med-team/dnarrange/-/commit/978a034b2890501a402d6e222b5dc5ba9b645727 You're receiving this email because of your account on salsa.debian.org.
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