Mandalorion

KO | EN

gitlite — search

#javascript #python #react #llm #machine-learning #linux #macos #java #awesome #kubernetes #ios #mcp #openai #open-source

(★ 9)

Pipeline to identify isoforms from full-length cDNA sequencing data

Mandalorion 최신버젼 다운로드

최종 버전 다운로드 (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# Mandalorion #
[![Github release](https://img.shields.io/github/tag/rvolden/Mandalorion.svg?label=Version)](https://github.com/rvolden/Mandalorion/tags)
[![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](http://perso.crans.org/besson/LICENSE.html)

Episode III.5: Rogue Isoforms

Takes R2C2/C3POa data and defines high confidence isoforms.

**This repository for Mandalorion is feature frozen. [The most up to date version of Mandalorion can be found here.](https://github.com/christopher-vollmers/Mandalorion)**

## Dependencies ##

- [minimap2](https://github.com/lh3/minimap2)
- [racon](https://github.com/isovic/racon)
- [emtrey](https://github.com/rvolden/emtrey) ([go](https://golang.org/dl/))
- [blat source](https://users.soe.ucsc.edu/~kent/src/blatSrc35.zip) or [blat executable](http://hgdownload.soe.ucsc.edu/admin/exe/)
- [medaka](https://github.com/nanoporetech/medaka)
- [abPOA](https://github.com/yangao07/abPOA)

The paths to these will need to be put into your config file [like this.](example_config) If you have the program installed or in your path already, replace the path with the name of the program.

## Usage ##
```bash
python3 Mandalorion.py [OPTIONS]
```

Running with default settings:
```bash
python3 Mandalorion.py -c config_file -p . -g gencodeV29.gtf -G hg38.fasta -a adapters.fasta -f R2C2_consensi.fasta -b R2C2_subreads.fastq
```

Required options:
```
-c  config file containing paths to required dependencies (above)
-p  output path
-g  annotation file (gtf)
-G  genome file (fasta)
-a  adapter file (fasta)
-f  R2C2 read file (fasta, can be comma separated list)
-b  R2C2 subread file (fastq, can be comma separated list)
```

Tweakable parameters:
```
-u  upstream buffer, defines leniency window for TSS and polyA definition (default 10)
-d  downstream buffer, defines leniency window for TSS and polyA definition (default 50)
-s  subsample consensus, defines how many random subreads are used to make isoforms (default 500)
-r  minimum ratio, proportion of reads that align to a locus required for an isoform (default 0.01)
-i  minimum internal ratio (default 1)
-R  minimum number of reads for an isoform (default 5)
-O  overhangs, defines bounds for unaligned bases on ends, format: min5',max5',min3',max3' (default 0,40,0,40)
-t  number of threads to use for minimap2 (default 4)
-e  ends, the ends of your sequences, format: 5prime,3prime (default 'ATGGG,AAAAA')
-I  minimum isoform length (default 500)
-n  minimum feature count (number of reads, default 2)
-w  splice site window (default 1)
-A  A proportion cutoff - isoforms with A content within a 30 nt window around the polyA higher than this will be discarded (default 0.5)
```

## Utils ##
These are the scripts used in the paper to do haplotype phasing and HLA analysis.

Mandalorion

Mandalorion 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

Mandalorion

Mandalorion 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

Download README