diff options
| -rw-r--r-- | biology/miniasm/DESCR | 22 | ||||
| -rw-r--r-- | biology/miniasm/Makefile | 30 | ||||
| -rw-r--r-- | biology/miniasm/PLIST | 6 | ||||
| -rw-r--r-- | biology/miniasm/distinfo | 6 |
4 files changed, 64 insertions, 0 deletions
diff --git a/biology/miniasm/DESCR b/biology/miniasm/DESCR new file mode 100644 index 00000000000..022259d7a3f --- /dev/null +++ b/biology/miniasm/DESCR @@ -0,0 +1,22 @@ +Miniasm is a very fast OLC-based *de novo* assembler for noisy long +reads. It takes all-vs-all read self-mappings (typically by minimap) +as input and outputs an assembly graph in the GFA format. Different +from mainstream assemblers, miniasm does not have a consensus step. It +simply concatenates pieces of read sequences to generate the final +unitig sequences. Thus the per-base error rate is similar to the raw +input reads. + +So far miniasm is in early development stage. It has only been tested +on a dozen of PacBio and Oxford Nanopore (ONT) bacterial data +sets. Including the mapping step, it takes about 3 minutes to assemble +a bacterial genome. Under the default setting, miniasm assembles 9 out +of 12 PacBio datasets and 3 out of 4 ONT datasets into a single +contig. + +Miniasm confirms that at least for high-coverage bacterial genomes, it +is possible to generate long contigs from raw PacBio or ONT reads +without error correction. It also shows that minimap can be used as a +read overlapper, even though it is probably not as sensitive as the +more sophisticated overlapers such as MHAP and DALIGNER. Coupled with +long-read error correctors and consensus tools, miniasm may also be +useful to produce high-quality assemblies. diff --git a/biology/miniasm/Makefile b/biology/miniasm/Makefile new file mode 100644 index 00000000000..698eb596c50 --- /dev/null +++ b/biology/miniasm/Makefile @@ -0,0 +1,30 @@ +# $NetBSD: Makefile,v 1.1 2021/05/26 18:44:44 brook Exp $ + +GITHUB_PROJECT= miniasm +GITHUB_TAG= refs/tags/v0.3 +DISTNAME= v0.3 +PKGNAME= ${GITHUB_PROJECT}-${DISTNAME:S,^v,,} +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_GITHUB:=lh3/} +DIST_SUBDIR= ${GITHUB_PROJECT} + +MAINTAINER= pkgsrc-users@NetBSD.org +HOMEPAGE= https://github.com/lh3/miniasm/ +COMMENT= OLC-based de novo assembler for long reads +LICENSE= mit + +WRKSRC= ${WRKDIR}/miniasm-0.3 +USE_TOOLS+= gmake +USE_LANGUAGES+= c + +INSTALLATION_DIRS+= bin ${PKGMANDIR}/man1 share/doc/miniasm + +do-install: + ${INSTALL} ${WRKSRC}/miniasm ${DESTDIR}${PREFIX}/bin + ${INSTALL} ${WRKSRC}/minidot ${DESTDIR}${PREFIX}/bin + ${INSTALL_DATA} ${WRKSRC}/miniasm.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1 + ${INSTALL_DATA} ${WRKSRC}/PAF.md ${DESTDIR}${PREFIX}/share/doc/miniasm + ${INSTALL_DATA} ${WRKSRC}/README.md ${DESTDIR}${PREFIX}/share/doc/miniasm + +.include "../../devel/zlib/buildlink3.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/miniasm/PLIST b/biology/miniasm/PLIST new file mode 100644 index 00000000000..a79b51b5b27 --- /dev/null +++ b/biology/miniasm/PLIST @@ -0,0 +1,6 @@ +@comment $NetBSD: PLIST,v 1.1 2021/05/26 18:44:44 brook Exp $ +bin/miniasm +bin/minidot +man/man1/miniasm.1 +share/doc/miniasm/PAF.md +share/doc/miniasm/README.md diff --git a/biology/miniasm/distinfo b/biology/miniasm/distinfo new file mode 100644 index 00000000000..378833a806c --- /dev/null +++ b/biology/miniasm/distinfo @@ -0,0 +1,6 @@ +$NetBSD: distinfo,v 1.1 2021/05/26 18:44:44 brook Exp $ + +SHA1 (miniasm/v0.3.tar.gz) = 11aa9dcfdf3d304fbc31d4be0246bb8d2108a70d +RMD160 (miniasm/v0.3.tar.gz) = f0352ea9952704a1b6df6eda1be5d9631c822a07 +SHA512 (miniasm/v0.3.tar.gz) = e5f622e079283d69bb878cbb9768f7522d279f89fc11f86a2b1fdade9e09e681e742d9e4be46bed4c864e4fef3d0d6760348c85cf1d5e029a36d96c45f885160 +Size (miniasm/v0.3.tar.gz) = 204805 bytes |