http://gmod.org/wiki/Diya

Address of the bookmark: https://sourceforge.net/projects/diyg/

Ref https://genomicsaotearoa.github.io/metagenomics_summer_school/day4/ex15_gene_annotation_part3/#overview-of-drampy-annotate-output 

Address of the bookmark: https://github.com/WrightonLabCSU/DRAM

Address of the bookmark: http://kobas.cbi.pku.edu.cn/

tax_id:
the unique identifier provided by NCBI Taxonomy
for the species or strain/isolate

GeneID:
the unique identifier for a gene
ASN1: geneid

Symbol:
the default symbol for the gene
ASN1: gene->locus

LocusTag:
the LocusTag value
ASN1: gene->locus-tag

Synonyms:
bar-delimited set of unofficial symbols for the gene

dbXrefs:
bar-delimited set of identifiers in other databases
for this gene. The unit of the set is database:value.
Note that HGNC and MGI include 'HGNC' and 'MGI', respectively,
in the value part of their identifier. Consequently,
dbXrefs for these databases will appear like:
HGNC:HGNC:1100
This would be interpreted as database='HGNC', value='HGNC:1100'
Example for MGI:
MGI:MGI:104537
This would be interpreted as database='MGI', value='MGI:104537'

chromosome:
the chromosome on which this gene is placed.
for mitochondrial genomes, the value 'MT' is used.

map location:
the map location for this gene

description:
a descriptive name for this gene

type of gene:
the type assigned to the gene according to the list of options
provided in https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn

Symbol from nomenclature authority:
when not '-', indicates that this symbol is from a
a nomenclature authority

Full name from nomenclature authority:
when not '-', indicates that this full name is from a
a nomenclature authority

Nomenclature status:
when not '-', indicates the status of the name from the
nomenclature authority (O for official, I for interim)

Other designations:
pipe-delimited set of some alternate descriptions that
have been assigned to a GeneID
'-' indicates none is being reported.

Modification date:
the last date a gene record was updated, in YYYYMMDD format

Feature type:
pipe-delimited set of annotated features and their classes or
controlled vocabularies, displayed as feature_type:feature_class
or feature_type:controlled_vocabulary, when appropriate; derived
from select feature annotations on RefSeq(s) associated with the
GeneID

Address of the bookmark: ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/

Address of the bookmark: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2002-3-12-research0082

Address of the bookmark: https://github.com/AlexanderLabWHOI/EUKulele

Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It should work on OSX, but please report any errors to maarten.reijnders@unil.ch or create an issue.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010075

Address of the bookmark: https://gitlab.com/mreijnders/crowdgo

Address of the bookmark: http://omega.omicsbio.org/

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. The 12 PacBio data sets are PacBio E. coli sample, ERS473430, ERS544009, ERS554120, ERS605484, ERS617393, ERS646601, ERS659581, ERS670327, ERS685285, ERS743109 and a deprecated PacBio E. coli data set. ONT data are acquired from the Loman Lab.

For a C. elegans PacBio data set (only 40X are used, not the whole dataset), miniasm finishes the assembly, including reads overlapping, in ~10 minutes with 16 CPUs. The total assembly size is 105Mb; the N50 is 1.94Mb. In comparison, the HGAP3produces a 104Mb assembly with N50 1.61Mb. This dotter plot gives a global view of the miniasm assembly (on the X axis) and the HGAP3 assembly (on Y). They are broadly comparable. Of course, the HGAP3 consensus sequences are much more accurate. In addition, on the whole data set (assembled in ~30 min), the miniasm N50 is reduced to 1.79Mb. Miniasm still needs improvements.

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.

Minimap and miniasm are ultrafast tools for (i) mapping and (ii) assembly. Designed for long, noisy reads, they do not have a correction or consensus step, and therefore the resulting assemblies are contiguous (i.e. long) but very noisy (i.e. full of errors)

We start with an all against all comparison:

minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz

Then we can assemble

miniasm -f reads.fq reads.paf.gz > reads.gfa

Convert GFA to FASTA:

awk '/^S/{print ">"$2"\n"$3}' reads.gfa | fold > reads.fa

And then count how many contigs:

grep ">" reads.fa | wc -l

# Download sample PacBio from the PBcR website
wget -O- http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz | tar zxf -
ln -s selfSampleData/pacbio_filtered.fastq reads.fq
# Install minimap and miniasm (requiring gcc and zlib)
git clone https://github.com/lh3/minimap && (cd minimap && make)
git clone https://github.com/lh3/miniasm && (cd miniasm && make)
# Overlap
minimap/minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz
# Layout
miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa

Address of the bookmark: https://github.com/lh3/miniasm