<![CDATA[BOL: MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)]]> https://bioinformaticsonline.com/bookmarks/view/34618/mashmap-a-fast-and-approximate-software-for-mapping-long-reads-pacbioont-or-assembly-to-reference-genomes? https://bioinformaticsonline.com/bookmarks/view/34618/mashmap-a-fast-and-approximate-software-for-mapping-long-reads-pacbioont-or-assembly-to-reference-genomes Tue, 12 Dec 2017 17:23:31 -0600 https://bioinformaticsonline.com/bookmarks/view/34618/mashmap-a-fast-and-approximate-software-for-mapping-long-reads-pacbioont-or-assembly-to-reference-genomes <![CDATA[MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)]]> MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but rather estimates a k-mer based Jaccard similarity using a combination of Winnowing and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is automatically determined given minimum local alignment length and identity thresholds. The efficiency of the algorithm improves as both of these thresholds are increased.

Address of the bookmark: https://github.com/marbl/MashMap

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34618/mashmap-a-fast-and-approximate-software-for-mapping-long-reads-pacbioont-or-assembly-to-reference-genomes#item-annotation-3432 Fri, 13 Jul 2018 17:21:42 -0500 https://bioinformaticsonline.com/bookmarks/view/34618/mashmap-a-fast-and-approximate-software-for-mapping-long-reads-pacbioont-or-assembly-to-reference-genomes#item-annotation-3432 <![CDATA[Comment by Jit]]> ➜ mashmap-Linux64-v2.0 git:(master) ✗ ./mashmap -h
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Mashmap is an approximate long read or contig mapper based on Jaccard
similarity
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Example usage:
$ mashmap -r ref.fa -q seq.fq [OPTIONS]
$ mashmap --rl reference_files_list.txt -q seq.fq [OPTIONS]

Available options
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-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