===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
miniasm-0.3+dfsg/README.md-6-ln -s selfSampleData/pacbio_filtered.fastq reads.fq
miniasm-0.3+dfsg/README.md:7:# Install minimap and miniasm (requiring gcc and zlib)
miniasm-0.3+dfsg/README.md-8-git clone https://github.com/lh3/minimap2 && (cd minimap2 && make)
miniasm-0.3+dfsg/README.md:9:git clone https://github.com/lh3/miniasm && (cd miniasm && make)
miniasm-0.3+dfsg/README.md-10-# Overlap for PacBio reads (or use "-x map-ont" for nanopore read overlapping)
##############################################
miniasm-0.3+dfsg/README.md-12-# Layout
miniasm-0.3+dfsg/README.md:13:miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa
miniasm-0.3+dfsg/README.md-14-```
##############################################
miniasm-0.3+dfsg/README.md-17-
miniasm-0.3+dfsg/README.md:18:Miniasm is a very fast OLC-based *de novo* assembler for noisy long reads. It
miniasm-0.3+dfsg/README.md-19-takes all-vs-all read self-mappings (typically by [minimap][minimap]) as input
miniasm-0.3+dfsg/README.md-20-and outputs an assembly graph in the [GFA][gfa] format. Different from
miniasm-0.3+dfsg/README.md:21:mainstream assemblers, miniasm does not have a consensus step. It simply
miniasm-0.3+dfsg/README.md-22-concatenates pieces of read sequences to generate the final [unitig][unitig]
##############################################
miniasm-0.3+dfsg/README.md-24-
miniasm-0.3+dfsg/README.md:25:So far miniasm is in early development stage. It has only been tested on
miniasm-0.3+dfsg/README.md-26-a dozen of PacBio and Oxford Nanopore (ONT) bacterial data sets. Including the
miniasm-0.3+dfsg/README.md-27-mapping step, it takes about 3 minutes to assemble a bacterial genome. Under
miniasm-0.3+dfsg/README.md:28:the default setting, miniasm assembles 9 out of 12 PacBio datasets and 3 out of
miniasm-0.3+dfsg/README.md-29-4 ONT datasets into a single contig. The 12 PacBio data sets are [PacBio E.
##############################################
miniasm-0.3+dfsg/README.md-37-For a *C. elegans* [PacBio data set][ce] (only 40X are used, not the whole
miniasm-0.3+dfsg/README.md:38:dataset), miniasm finishes the assembly, including reads overlapping, in ~10
miniasm-0.3+dfsg/README.md-39-minutes with 16 CPUs. The total assembly size is 105Mb; the N50 is 1.94Mb. In
miniasm-0.3+dfsg/README.md-40-comparison, the [HGAP3][hgap] produces a 104Mb assembly with N50 1.61Mb. [This
miniasm-0.3+dfsg/README.md:41:dotter plot][ce-img] gives a global view of the miniasm assembly (on the X
miniasm-0.3+dfsg/README.md-42-axis) and the HGAP3 assembly (on Y). They are broadly comparable. Of course,
miniasm-0.3+dfsg/README.md-43-the HGAP3 consensus sequences are much more accurate. In addition, on the whole
miniasm-0.3+dfsg/README.md:44:data set (assembled in ~30 min), the miniasm N50 is reduced to 1.79Mb. Miniasm
miniasm-0.3+dfsg/README.md-45-still needs improvements.
miniasm-0.3+dfsg/README.md-46-
miniasm-0.3+dfsg/README.md:47:Miniasm confirms that at least for high-coverage bacterial genomes, it is
miniasm-0.3+dfsg/README.md-48-possible to generate long contigs from raw PacBio or ONT reads without error
##############################################
miniasm-0.3+dfsg/main.c-75- if (argc == optind) {
miniasm-0.3+dfsg/main.c:76: fprintf(stderr, "Usage: miniasm [options] <in.paf>\n");
miniasm-0.3+dfsg/main.c-77- fprintf(stderr, "Options:\n");
##############################################
miniasm-0.3+dfsg/misc/demo-ecoli-pacbio.sh-8-
miniasm-0.3+dfsg/misc/demo-ecoli-pacbio.sh:9:# Install minimap and miniasm (requiring gcc and zlib)
miniasm-0.3+dfsg/misc/demo-ecoli-pacbio.sh-10-git clone https://github.com/lh3/minimap && (cd minimap && make)
miniasm-0.3+dfsg/misc/demo-ecoli-pacbio.sh:11:git clone https://github.com/lh3/miniasm && (cd miniasm && make)
miniasm-0.3+dfsg/misc/demo-ecoli-pacbio.sh-12-
##############################################
miniasm-0.3+dfsg/misc/demo-ecoli-pacbio.sh-16-# Layout
miniasm-0.3+dfsg/misc/demo-ecoli-pacbio.sh:17:miniasm/miniasm -f reads.fq reads.paf.gz > utg.gfa
miniasm-0.3+dfsg/misc/demo-ecoli-pacbio.sh-18-
##############################################
miniasm-0.3+dfsg/misc/demo-worm-pacbio.sh-44-
miniasm-0.3+dfsg/misc/demo-worm-pacbio.sh:45:# Install minimap and miniasm (requiring gcc and zlib)
miniasm-0.3+dfsg/misc/demo-worm-pacbio.sh-46-git clone https://github.com/lh3/minimap && (cd minimap && make)
miniasm-0.3+dfsg/misc/demo-worm-pacbio.sh:47:git clone https://github.com/lh3/miniasm && (cd miniasm && make)
miniasm-0.3+dfsg/misc/demo-worm-pacbio.sh-48-
##############################################
miniasm-0.3+dfsg/misc/demo-worm-pacbio.sh-52-# Layout
miniasm-0.3+dfsg/misc/demo-worm-pacbio.sh:53:miniasm/miniasm -f $prefix.fa.gz $prefix.paf.gz > $prefix.gfa 2> $prefix.gfa.log
miniasm-0.3+dfsg/misc/demo-worm-pacbio.sh-54-
##############################################
miniasm-0.3+dfsg/debian/changelog:1:miniasm (0.3+dfsg-2) unstable; urgency=medium
miniasm-0.3+dfsg/debian/changelog-2-
##############################################
miniasm-0.3+dfsg/debian/changelog-10-
miniasm-0.3+dfsg/debian/changelog:11:miniasm (0.3+dfsg-1) unstable; urgency=medium
miniasm-0.3+dfsg/debian/changelog-12-
##############################################
miniasm-0.3+dfsg/debian/changelog-17-
miniasm-0.3+dfsg/debian/changelog:18:miniasm (0.2+dfsg-3) unstable; urgency=medium
miniasm-0.3+dfsg/debian/changelog-19-
##############################################
miniasm-0.3+dfsg/debian/changelog-27-
miniasm-0.3+dfsg/debian/changelog:28:miniasm (0.2+dfsg-2) unstable; urgency=medium
miniasm-0.3+dfsg/debian/changelog-29-
##############################################
miniasm-0.3+dfsg/debian/changelog-36-
miniasm-0.3+dfsg/debian/changelog:37:miniasm (0.2+dfsg-1) unstable; urgency=medium
miniasm-0.3+dfsg/debian/changelog-38-
##############################################
miniasm-0.3+dfsg/debian/changelog-43-
miniasm-0.3+dfsg/debian/changelog:44:miniasm (0.2-1) unstable; urgency=low
miniasm-0.3+dfsg/debian/changelog-45-
##############################################
miniasm-0.3+dfsg/debian/control-19-Description: ultrafast de novo assembler for long noisy DNA sequencing reads
miniasm-0.3+dfsg/debian/control:20: Miniasm is an experimental very fast OLC-based de novo assembler for noisy
miniasm-0.3+dfsg/debian/control-21- long reads. It takes all-vs-all read self-mappings (typically by minimap)
miniasm-0.3+dfsg/debian/control-22- as input and outputs an assembly graph in the GFA format. Different from
miniasm-0.3+dfsg/debian/control:23: mainstream assemblers, miniasm does not have a consensus step. It simply
miniasm-0.3+dfsg/debian/control-24- concatenates pieces of read sequences to generate the final unitig sequences.
##############################################
miniasm-0.3+dfsg/debian/install:1:miniasm /usr/bin
##############################################
miniasm-0.3+dfsg/debian/patches/hardening-12- OBJS= sys.o sdict.o paf.o asg.o common.o hit.o asm.o
miniasm-0.3+dfsg/debian/patches/hardening:13: PROG= miniasm minidot
miniasm-0.3+dfsg/debian/patches/hardening-14-@@ -9,15 +8,15 @@ LIBS= -lm -lz -lpthread
##############################################
miniasm-0.3+dfsg/debian/patches/spelling-7- length of edge v->w and maxovlp(v)=max_w{overlap(v->w)} be the length of
miniasm-0.3+dfsg/debian/patches/spelling:8: largest overlap. Miniasm drops overlap v->w if overlap(v->w)/maxovlp(v) is below
miniasm-0.3+dfsg/debian/patches/spelling:9:-a threshold controled by this option. Miniasm applies
miniasm-0.3+dfsg/debian/patches/spelling:10:+a threshold controlled by this option. Miniasm applies
miniasm-0.3+dfsg/debian/patches/spelling-11- .I nRounds
##############################################
miniasm-0.3+dfsg/debian/tests/run-1-#!/bin/sh
miniasm-0.3+dfsg/debian/tests/run:2:# autopkgtest check: Run miniasm on example data
miniasm-0.3+dfsg/debian/tests/run-3-# Author: Sascha Steinbiss <sascha@steinbiss.name>
##############################################
miniasm-0.3+dfsg/debian/tests/run-21-minimap -Sw5 -L100 -m0 reads.fasta reads.fasta | gzip -1 > out.paf.gz
miniasm-0.3+dfsg/debian/tests/run:22:miniasm -f reads.fasta out.paf.gz > out.gfa
miniasm-0.3+dfsg/debian/tests/run-23-
##############################################
miniasm-0.3+dfsg/.pc/hardening/Makefile-5-OBJS= sys.o sdict.o paf.o asg.o common.o hit.o asm.o
miniasm-0.3+dfsg/.pc/hardening/Makefile:6:PROG= miniasm minidot
miniasm-0.3+dfsg/.pc/hardening/Makefile-7-LIBS= -lm -lz -lpthread
##############################################
miniasm-0.3+dfsg/.pc/spelling/miniasm.1:1:.TH miniasm 1 "23 July 2018" "miniasm-0.3 (r179)" "Bioinformatics tools"
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-2-
##############################################
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-4-.PP
miniasm-0.3+dfsg/.pc/spelling/miniasm.1:5:miniasm - de novo assembler for long read sequences
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-6-
##############################################
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-46-.PP
miniasm-0.3+dfsg/.pc/spelling/miniasm.1:47:Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-48-takes all-vs-all read self-mappings in the PAF format as input and outputs an
##############################################
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-142-.I INT
miniasm-0.3+dfsg/.pc/spelling/miniasm.1:143:reads [4]. Miniasm may try to remove small unitigs at various steps.
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-144-
##############################################
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-147-Read sequence file in FASTA or FASTQ format for generating unitig sequences
miniasm-0.3+dfsg/.pc/spelling/miniasm.1:148:[null]. If this option is absent, miniasm produces a GFA output without
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-149-sequences.
##############################################
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-154-length of edge v->w and maxovlp(v)=max_w{overlap(v->w)} be the length of
miniasm-0.3+dfsg/.pc/spelling/miniasm.1:155:largest overlap. Miniasm drops overlap v->w if overlap(v->w)/maxovlp(v) is below
miniasm-0.3+dfsg/.pc/spelling/miniasm.1:156:a threshold controled by this option. Miniasm applies
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-157-.I nRounds
##############################################
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-205-.PP
miniasm-0.3+dfsg/.pc/spelling/miniasm.1:206:Miniasm reads mapping positions in the Pairwise mApping Format (PAF), which is
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-207-a TAB-delimited text format with each line consisting of at least 12 fields as
##############################################
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-235-.PP
miniasm-0.3+dfsg/.pc/spelling/miniasm.1:236:Miniasm outputs the assembly in the Graphical Fragment Assembly format (GFA).
miniasm-0.3+dfsg/.pc/spelling/miniasm.1-237-It is a line based TAB-delimited format, with the leading letter indicates the
##############################################
miniasm-0.3+dfsg/Makefile-4-OBJS= sys.o sdict.o paf.o asg.o common.o hit.o asm.o
miniasm-0.3+dfsg/Makefile:5:PROG= miniasm minidot
miniasm-0.3+dfsg/Makefile-6-LIBS= -lm -lz -lpthread
##############################################
miniasm-0.3+dfsg/miniasm.1:1:.TH miniasm 1 "23 July 2018" "miniasm-0.3 (r179)" "Bioinformatics tools"
miniasm-0.3+dfsg/miniasm.1-2-
##############################################
miniasm-0.3+dfsg/miniasm.1-4-.PP
miniasm-0.3+dfsg/miniasm.1:5:miniasm - de novo assembler for long read sequences
miniasm-0.3+dfsg/miniasm.1-6-
##############################################
miniasm-0.3+dfsg/miniasm.1-46-.PP
miniasm-0.3+dfsg/miniasm.1:47:Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It
miniasm-0.3+dfsg/miniasm.1-48-takes all-vs-all read self-mappings in the PAF format as input and outputs an
##############################################
miniasm-0.3+dfsg/miniasm.1-142-.I INT
miniasm-0.3+dfsg/miniasm.1:143:reads [4]. Miniasm may try to remove small unitigs at various steps.
miniasm-0.3+dfsg/miniasm.1-144-
##############################################
miniasm-0.3+dfsg/miniasm.1-147-Read sequence file in FASTA or FASTQ format for generating unitig sequences
miniasm-0.3+dfsg/miniasm.1:148:[null]. If this option is absent, miniasm produces a GFA output without
miniasm-0.3+dfsg/miniasm.1-149-sequences.
##############################################
miniasm-0.3+dfsg/miniasm.1-154-length of edge v->w and maxovlp(v)=max_w{overlap(v->w)} be the length of
miniasm-0.3+dfsg/miniasm.1:155:largest overlap. Miniasm drops overlap v->w if overlap(v->w)/maxovlp(v) is below
miniasm-0.3+dfsg/miniasm.1:156:a threshold controlled by this option. Miniasm applies
miniasm-0.3+dfsg/miniasm.1-157-.I nRounds
##############################################
miniasm-0.3+dfsg/miniasm.1-205-.PP
miniasm-0.3+dfsg/miniasm.1:206:Miniasm reads mapping positions in the Pairwise mApping Format (PAF), which is
miniasm-0.3+dfsg/miniasm.1-207-a TAB-delimited text format with each line consisting of at least 12 fields as
##############################################
miniasm-0.3+dfsg/miniasm.1-235-.PP
miniasm-0.3+dfsg/miniasm.1:236:Miniasm outputs the assembly in the Graphical Fragment Assembly format (GFA).
miniasm-0.3+dfsg/miniasm.1-237-It is a line based TAB-delimited format, with the leading letter indicates the