BOL: Related items

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Poonam Mahapatra — Mon, 04 Jun 2018 03:45:15 -0500

One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies, including LTR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics for each TE family (number of TE copies, genome coverage...) Ambiguous cases such as nested TE can be assembled into copies automatically or manually Allow for working with a TE user-defined library Allow for working with only a user-chosen set of TE families http://doua.prabi.fr/software/one-code-to-find-them-all

Address of the bookmark: http://doua.prabi.fr/software/one-code-to-find-them-all

LSC :a long read error correction tool

Jit — Thu, 02 Aug 2018 07:39:46 -0500

Getting Started

These simple steps will help you integrate LSC into your transcriptomics analysis pipeline.

Read the LSC_requirements for running LSC.
Download and set-up the LSC package.
Follow the tutorial to see how LSC works on some example data.
Read the manual if anything is unclear.
You're ready, Happy LSCing!

Latest publication

Kin Fai Au, Jason Underwood, Lawrence Lee and Wing Hung Wong
Improving PacBio Long Read Accuracy by Short Read Alignment [Manuscript]
PLoS ONE 2012. 7(10): e46679. doi:10.1371/journal.pone.0046679

Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads

Jit — Mon, 20 Aug 2018 04:08:50 -0500

Here is the command to run the tool:

python finisherSC.py destinedFolder mummerPath

If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC.

python finisherSC.py -par 20 destinedFolder mummerPath

Sometimes, if the names of raw reads and contigs consists of special characters/formats, FinisherSC/MUMmer may not parse them correctly. In that case, you want to have a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads.fasta using the following command.

    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' raw_reads.fasta > newRaw_reads.fasta
    cp newRaw_reads.fasta raw_reads.fasta
    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' contigs.fasta > newContigs.fasta
    cp newContigs.fasta contigs.fasta

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

rHAT: a seed-and-extension-based noisy long read alignment tool

Abhimanyu Singh — Sun, 23 Sep 2018 05:12:22 -0500

rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.

Address of the bookmark: https://github.com/dfguan/rHAT

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

BioJoker — Sun, 20 Jan 2019 06:34:36 -0600

ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome.

Address of the bookmark: https://github.com/shinout/clipcrop

vt: a variant tool set that discovers short variants from Next Generation Sequencing data.

Jit — Tue, 28 Jan 2020 03:44:43 -0600

vt is a variant tool set that discovers short variants from Next Generation Sequencing data.

https://genome.sph.umich.edu/wiki/Vt

https://github.com/atks/vt

Address of the bookmark: https://genome.sph.umich.edu/wiki/Vt

Filtlong: quality filtering tool for long reads

Radha Agarkar — Wed, 13 May 2020 10:23:55 -0500

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

Filtlong builds into a stand-alone executable:

git clone https://github.com/rrwick/Filtlong.git
cd Filtlong
make -j
bin/filtlong -h

Address of the bookmark: https://github.com/rrwick/Filtlong

Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies

Jit — Tue, 30 Jun 2020 21:40:52 -0500

Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a standalone tool that takes two genome assemblies and a reference annotation as input and outputs an annotation of the target genome.

Address of the bookmark: https://github.com/agshumate/Liftoff

vsFilt: A tool to improve virtual screening by structural filtration of docking poses

Neel — Wed, 25 Nov 2020 02:39:16 -0600

The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide range of interaction types that are known to be involved in molecular recognition, including hydrogen and halogen bonds, ionic interactions, hydrophobic contacts, π-stacking, and cation-π interactions. The web-server can process large libraries of up to 150’000 docked ligand poses. The results are web-based and can be operated on-line using the built-in HTML5 interactive analysis tools, or can be downloaded for a local use. The vsFilt is freely available on-line, no login required.

Address of the bookmark: https://biokinet.belozersky.msu.ru/vsfilt

JumboDB: tool for de Bruijn graph construction

BioStar — Tue, 17 Aug 2021 13:33:46 -0500

jumboDB tool for fast de Bruijn graph construction from long sequences (reads or genomes) with very low error rate. JumboDB is not a genome assembler by itself but rather a subroutine that translates a set of reads into compressed de Bruijn graph.

More at https://github.com/AntonBankevich/jumboDB

Address of the bookmark: https://github.com/AntonBankevich/jumboDB