msscaf

Multiple-source scaffolder

This tool scaffold contigs using several sources. To date, msscaf supports:

• long reads (mapped to the contigs, in .paf format, for instance mapped with minimap2);
• 10X (mapped with LongRanger);
• Hi-C (in .hic format).

msscaf is written in R. No previous knowledge of R is required. You can adapt the following pipe-line to suit your needs.

Simply get R installed, and start it with the command

 R

Pipe-line

Download package:

if (!("devtools" %in% rownames(installed.packages()))) install.packages("devtools")
devtools::install_github("mzytnicki/msscaf")

Load package:

library("msscaf")

Read data:

resolution  <- 10000
hicFileName <- "/path/to/hic/file.hic"
hicData     <- parseHicFile(hicFileName, resolution)
# Alternatively, the "parseCoolFile" is available for the .cool/.mcool formats
ontFileName <- "/path/to/long/reads.paf"
ontData     <- parsePafFile(ontFileName, resolution)
bamFileName <- "/path/to/long/10X.bam"
bamData     <- parseBamFile(bamFileName, resolution)

Load data:

contigFileName <- "/path/to/contigs.fa"
scaffolder     <- msscaf(contigFileName, resolution)
scaffolder     <- addExp(scaffolder, ontData, "ONT")
scaffolder     <- addExp(scaffolder, hicData, "HiC")
scaffolder     <- addExp(scaffolder, bamData, "10X")

Estimate distributions:

scaffolder <- estimateDistributions(scaffolder)
scaffolder <- cleanData(scaffolder)

Find breaks:

pvalue     <- 0.01
scaffolder <- findBreaks(scaffolder, pvalue)
scaffolder <- splitChromosomes(scaffolder)

Find merges:

scaffolder <- findJoins(scaffolder, pvalue)
scaffolder <- scaffold(scaffolder)

Write scaffolds to file:

outputFileName <- "/path/to/output/scaffolds.fa"
Biostrings::writeXStringSet(Biostrings::DNAStringSet(scaffolder@sequences), outputFileName)

Accessing data

The breaks can be accessed with:

scaffolder@breaks

The joins can be accessed with:

scaffolder@joins

Visualization

The whole matrices can be displayed with:

plot.msscaf(scaffolder)

One contig/scaffold (here, ctg1) can be displayed with:

plot.msscaf(scaffolder, ref1 = ctg1)

The interaction between two contig/scaffolds (here, ctg1 and ctg2) can be displayed with:

plot.msscaf(scaffolder, ref1 = ctg1, ref2 = ctg2)

One break (located at position ctg1:100) can be displayed with:

plot.msscafBreak(scaffolder, ref = ctg1, bin = 100)

One join (joining the right ends of ctg1 and ctg2) can be displayed with:

plot.msscafJoin(scaffolder, ref1 = ctg1, ref2 = ctg2, after1 = TRUE, after2 = TRUE)