BOL: Related items

SVfinder: Tool for detecting genomic rearrangement form DNA-seq data

Robert M Willioms — Thu, 14 Dec 2017 15:51:40 -0600

SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

Address of the bookmark: https://github.com/cauyrd/SVfinder

EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes

Surabhi Chaudhary — Sat, 12 May 2018 07:26:59 -0500

SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in eukaryotes.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4724-8

Address of the bookmark: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4724-8

minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences

Jit — Wed, 20 Jun 2018 07:55:29 -0500

git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and then map ./minimap2 -d MT-human.mmi test/MT-human.fa ./minimap2 -a MT-human.mmi test/MT-orang.fa > test.sam # use presets (no test data) ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio genomic reads ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads ./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam # short genomic paired-end reads ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads ./minimap2 -ax splice -k14 -uf ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap ./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf # Nanopore read overlap # man page for detailed command line options man ./minimap2.1

Address of the bookmark: https://github.com/lh3/minimap2

FGENESH - Program for predicting multiple genes in genomic DNA sequences

BioStar — Thu, 20 Dec 2018 11:55:08 -0600

FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et al. (2002) Science 296:79) and was used to produce 87% of all high-evidence predicted genes (Goff et al. (2002) Science 296:79).

Address of the bookmark: http://www.softberry.com/berry.phtml?topic=fgenesh&group=help&subgroup=gfind

RepeatModeler2: automated genomic discovery of transposable element families

Neel — Mon, 02 Dec 2019 06:52:29 -0600

RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/RepeatModeler, https://github.com/Dfam-consortium/TETools).

Address of the bookmark: https://github.com/Dfam-consortium/TETools

dna2bit: an ultra-fast and accurate genomic distance estimation software

Neel — Wed, 13 Aug 2025 19:56:21 -0500

dna2bit: an ultra-fast and accurate genomic distance estimation software

dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation.

Address of the bookmark: https://github.com/lijuzeng/dna2bit

BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly

Jit — Mon, 22 May 2017 05:43:51 -0500

This tool is for users to upgrade their metagenomics assemblies using long reads. This includes fixing mis-assemblies and scaffolding/gap-filling. If you encounter any issues, please contact me at kklam@eecs.berkeley.edu. My name is Ka-Kit Lam.

https://github.com/kakitone/MetaFinisherSC

https://github.com/kakitone/BIGMAC

Address of the bookmark: https://github.com/kakitone/BIGMAC

Metabuli 분리 improves metagenomic read classification

Abhi — Sat, 03 Jun 2023 20:15:04 -0500

Metabuli 분리 improves metagenomic read classification through metamers, DNA-AA k-mers, to be sensitive and specific, recovering 99% and 98% of DNA or AA classifiers.

Metabuli is metagenomic classifier that jointly analyze both DNA and amino acid (AA) sequences. DNA-based classifiers can make specific classifications, exploiting point mutations to distinguish close taxa. AA-based classifiers have higher sensitivity in detecting homology between query and reference sequences, leverageing higher conservation of AA sequences. Metabuli combines the information of both sequence types using a novel k-mer structure, metamer, to enable both specific and sensitive characterization of metagenomic samples. In addition, it can classify reads against a database of any size as long as it fits in the hard disk.

Address of the bookmark: https://github.com/steineggerlab/Metabuli

Search Shell Command History

Rahul Nayak — Thu, 12 Jun 2014 17:43:34 -0500

We use couple of hundreads of command in daily basis. Most of them are actually repeated several time. The question remain open how do I search old command history under bash shell and modify or reuse it?

Now a days almost all modern shell allows you to search command history if enabled by user. Use history command to display the history list with line numbers. Lines listed with with a * have been modified by user.

Shell history search command

Type history at a shell prompt:
$ history

It will display the list of all used commandline history with an serial number.

To search particular command, enter:
$ history | grep command-name
$ history | egrep -i 'scp|ssh|ftp'
Emacs Line-Edit Mode Command History Searching

To get previous command containing string, hit [CTRL]+[r] followed by search string:

(reverse-i-search):

To get previous command, hit [CTRL]+[p]. You can also use up arrow key.

CTRL-p

To get next command, hit [CTRL]+[n]. You can also use down arrow key.

CTRL-n

fc command

Apart from hostory command there are fc command to extract the command from history. The fc stands for either "find command" or "fix command.

For example list last 10 command, enter:
$ fc -l 10
To list commands 130 through 150, enter:
$ fc -l 130 150
To list all commands since the last command beginning with ssh, enter:
$ fc -l ssh
You can edit commands 1 through 5 using vi text editor, enter:
$ fc -e vi 1 5

Delete command history

The -c option causes the history list to be cleared by deleting all of the entries:
$ history -c

Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search

Jit — Tue, 28 Jan 2020 03:34:23 -0600

Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only

Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be unpractical for large error prone genomes which makes the assembly process produce an excessive number of false positive cycles. Our solution is to search the graph in multicores shared memory parallel mode using graph decomposition then use filtering method to generate good quality SNPs.

https://arxiv.org/abs/1809.06700

https://github.com/redayounsi/2KP2P

/2kp2omp/bin/main_2kp2_K63_C2 -i fastq_files.txt -o fungus_bub.fasta -r stat_fungus.txt -c cov_fungus_hash.txt -k 63 -h 20 -b 100 -g 600 -l 100 -f 16 -t 5.0 -x 1 -v 0 -p 1 -y 1 -u 1

Address of the bookmark: https://github.com/redayounsi/2KP2P