Latest activity
Jit bookmarked MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to...Comments- Jit 3028 days ago
➜ mashmap-Linux64-v2.0 git:(master) ✗ ./mashmap -h
-----------------
Mashmap is an approximate long read or contig mapper based on Jaccard
similarity
-----------------
Example usage:
$ mashmap -r ref.fa -q seq.fq [OPTIONS]
$ mashmap --rl reference_files_list.txt -q seq.fq [OPTIONS]Available options
-----------------
-h, --help
Print this help page-r <value>, --ref <value>
an input reference file (fasta/fastq)[.gz]--refList <value>, --rl <value>
a file containing list of reference files, one per line-q <value>, --query <value>
an input query file (fasta/fastq)[.gz]--ql <value>, --queryList <value>
a file containing list of query files, one per line-s <value>, --segLength <value>
mapping segment length [default : 5,000]
sequences shorter than segment length will be ignored--noSplit
disable splitting of input sequences during mapping [enabled by default]--perc_identity <value>, --pi <value>
threshold for identity [default : 85]-t <value>, --threads <value>
count of threads for parallel execution [default : 1]-o <value>, --output <value>
output file name [default : mashmap.out]-k <value>, --kmer <value>
kmer size <= 16 [default : 16]-f <value>, --filter_mode <value>
filter modes in mashmap: 'map', 'one-to-one' or 'none' [default: map]
'map' computes best mappings for each query sequence
'one-to-one' computes best mappings for query as well as reference sequence
'none' disables filtering
- Jit commented on a bookmark List of Bioinformatics Vacancy, Jobs, Opportunity websites
- Jit created a new bio-script Reformat the file names with Perl
- Jit posted a new ad in the ResearchLabs Talkowski Laboratory
- Neel bookmarked BBTools User Guide
- Poonam Mahapatra posted to the wire
- Poonam Mahapatra created a page Converting BLAST output into CSV
- Rahul Agarwal posted to the wire
- Jit bookmarked Synima: Synteny Imaging tool
- Rahul Agarwal posted to the wire
- Rahul Agarwal posted to the wire
- Rahul Nayak posted to the wire
- Rahul Nayak bookmarked R googleVis examples
- Rahul Nayak created a new bio-script Calculate Dinucleotide Frequency with Perl
- Abhimanyu Singh commented on a bookmark List of Bioinformatics Vacancy, Jobs, Opportunity websites
- Jit bookmarked Mugsy: multiple whole genome alignment toolComments
- BioStar 2191 days ago
- Set up the environment
bash source /path/to/install/mugsyenv.sh
- Run mugsy
mugsy --directory /data/output --prefix mygenomes genome1.fasta genome2.fasta genome3.fasta
This example will align three genomes and output a file /data/output/mygenomes.maf. The --directory setting is also used for storing temporary files during the run.
The prefix of each input filename will be used as the genome name in the output files (eg. genome1 from genome1.fsa). Header lines in the FASTA files should not contain ':' or '-' to avoid parsing problems.- View or parse MAF output
The output of Mugsy is Multiple Alignment Format (MAF).
One option for browsing is GMAJ, which provides a reference-based stand-alone viewer for MAF files.java -jar gmaj.jar mygenomes.maf
- Set up the environment
