Another file which is of interest is scaffolds_FINAL.agp, which is the agp style output for the scaffolds describing the assignment, orientation and ordering of contigs along the scaffolds. The files you will be interested in are scaffolds_FINAL.fasta, which contains the sequences for the scaffolds generated by the algorithm. SALSA is an iterative algorithm, so it generates files for each iteration. SALSA generates a bunch of files in the output folder. You can still run SALSA with -u option not set. Note here that using unitigs_tiling.bed is not mandatory to run SALSA in this mode. Python run_pipeline.py -a unitigs.fasta -l -b alignment.bed -e -o scaffolds -m yes -g unitigs_graph.gfa
#Salsa salsa code#
Once you prepare the bed file as described above, the code can be run as follows: This is the minimum input you will require Suppose you only have contig sequences generated. 1) I have contig sequences and the alignment bam file You can also specify DNASE as an enzyme if you use an enzyme-free prep, e.g. For example, if you use MboI in the Hi-C protocol ,then you would specify it as -e GATC. Note that you need to specify the actual sequence of the cutting site for a restriction enzyme and not the enzyme name. If multiple enzymes were used, they can specified by separating with comma without space, like -e GATC,AAGCTT. You will need to specify the restriction site for the enzyme which was used for Hi-C experiment while running SALSA in -e option. We use the enzyme frequency in contigs to normalize the Hi-C interaction frequency. Hi-C experiments can use different restriction enzymes. You can use this file for contig lengths while running SALSA. This will generate as an input for -l option. To align and postprocess the alignments, you can use the pipeline released by Arima Genomics which can be found here. Since Hi-C reads and alignments contain experimental artifacts, the alignments needs some postprocessing. Once you have bam file, you can run following commands to get the bam Also, SALSA requires bed file to be sorted by the read name, rather than the alignment coordinates. This can be done using the bamToBed command from the Bedtools package. We recommend using BWA or BOWTIE2 aligner to map reads. To start the scaffolding, first step is to map reads to the assembly. Set this option to "yes" if you want to find s EXP, -exp EXP Expected Genome size of the assembled genome x DUP, -dup DUP File containing duplicated contig information i ITER, -iter ITER Number of iterations to run, default = 3 Minimum contig length to scaffold, default=1000 b BED, -bed BED Bed file of alignments sorted by read names Path to initial assembly, headers must not contain ':' h, -help show this help message and exit Usage: run_pipeline.py -a ASSEMBLY -l LENGTH -b BED We provide options to use different information provided by the assembly to use for the scaffolding. Some assemblers output assembly graph as well along with the contig sequences. The new version of SALSA has been designed to consider several use cases depending on the input.
#Salsa salsa how to#
bioRxiv, p.261149 Linkįor any queries, please either ask on github issue page or send an email to Jay Ghurye ( How to run the code? Integrating Hi-C links with assembly graphs for chromosome-scale assembly. Ghurye, J., Rhie, A., Walenz, B.P., Schmitt, A., Selvaraj, S., Pop, M., Phillippy, A.M. Scaffolding of long read assemblies using long range contact information. Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C.
If you consider using this tool, please cite our publication which describes the methods used for scaffolding. Learn more about Instacart pricing here.To run the code, you will need Python 2.7, BOOST libraries and Networkx(version lower than 1.2). Pick up orders have no service fees, regardless of non-Express or Express membership. Express membership waives this like it would a delivery fee. Instacart pickup cost: - There may be a "pickup fee" (equivalent to a delivery fee for pickup orders) on your pick up order that is typically $1.99 for non-Express members. With an optional Instacart Express membership, you can get $0 delivery fee on every order over $35 and lower service fees too. 100% of your tip goes directly to the shopper who delivers your order. It's a great way to show your shopper appreciation and recognition for excellent service. Tipping is optional but encouraged for delivery orders. Orders containing alcohol have a separate service fee. Service fees vary and are subject to change based on factors like location and the number and types of items in your cart. Fees vary for one-hour deliveries, club store deliveries, and deliveries under $35. Here's a breakdown of Instacart delivery cost: - Delivery fees start at $3.99 for same-day orders over $35.