SCUBAT

KO | EN

gitlite — search

#python #hacktoberfest #react #typescript #llm #machine-learning #rust #linux #macos #windows #kubernetes #awesome-list #ios #open-source

(★ 8)

Scaffolding Contigs Using Blat And Transcripts

SCUBAT 최신버젼 다운로드

최종 버전 다운로드 (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

#Overview

SCUBAT (Scaffolding Contigs Using BLAT And Transcripts) uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.

#Software Requirements

[CAP3](http://seq.cs.iastate.edu/cap3.html) - to assemble scaffolds

[GNU parallel](http://www.gnu.org/software/parallel/) - to run the CAP3 assemblies in parallel

#Data requirments

1. A genome in FASTA format
2. A set  of transcripts in FASTA format
3. A [BLAT](http://genome.ucsc.edu/FAQ/FAQblat.html#blat3) psl file aligning the transcripts to the genome

#Quick guide

`scubat.pl -t genome.fa -q transcripts.fa -p blat_output.psl`

To see all options just run `scubat.pl`

#Details

SCUBAT procedes via 6 steps:

###1)  Align the transcripts to the genome (not part of the script):

- Externally - Use BLAT to align the transcripts to the genome with psl output, e.g. `blat -t=dna genome.fa -q=dna transcripts.fa -noHead out.psl`

###2)  Identify informative split transcripts:

- All transcripts that mapped to more than one contig are flagged. Each mapping is then analysed to identify those that map consecutive non-overlapping sections of the transcript on separate contigs allowing for an overlap buffer zone of up to 20bp.

###3) Create scaffolds:

- Each transcript-contig complex is assembled by orientating the contigs based on the
BLAT information and adding 10 N’s in-between the contigs.

###4) Cluster scaffolds into groups and assemble:

- The contigs used in each transcript-contig complex are then cross-referenced and any complexes sharing a contig are grouped. Groups are then assembled using CAP3 with default parameters.

###5) Filter the assemblies:

- The assemblies are parsed to identify successful assembly events. Failed assemblies are identified and the largest complex kept, the remainder removed.

###6) Create new contig set:

- A new contig set is generated using the successful CAP3 assemblies, the remaining complexes and any contig not involved.

SCUBAT

SCUBAT 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

SCUBAT

SCUBAT 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

Download README