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| Name | Modified | Size | Downloads / Week |
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| README | 2015-06-04 | 3.1 kB | |
| ngs-suite-1.2-source.tar.gz | 2015-06-03 | 509.5 kB | |
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NGS-SUITE The aim is to have different efficient programs that perform simple but powerful tasks for NGS data. The implementation is divided in two parts: the core algorithms and data structures are implemented in a library called "libbiocpp". This last is an open source library written in C++11 that can be easily adapted to be used and extended and it is independent with respect to the final user objectives. The tools in "ngs-suite" take advantage of the library to solve user-oriented problems like fastq/bam statistics, data filtering, computing coverage profiles and so on. "libbiocpp" can be downloaded from http://libbiocpp.sf.net "ngs-suite" can be downloaded from http://ngs-suite.sf.net ============================= FASTA/FASTQ related programs. They work with multi-fasta or multi-fastq input files with format and compression auto-detection. Where relevant, they work with single-end and paired-ends files. ns-fasta-extract Given a list of names and (optional) start and stop position, extract the regions from the input file(s). ns-fastq-filter Given a set of adapters, remove the adapters from the file(s). ns-fastq-split Split file(s) into smaller fixed-length sets. ns-fastq2kmers Compute kmers profile from a fastq file. It can works with BS-Seq data. ns-fastq-overlap Given a paired-ends set of file, for each paired records compute the overlap (useful when inserted size is smaller than sequenced size). ns-fastq-stats Compute some statistics about FASTA/FASTQ files. ns-smallrna-trimming Remove adapters from 3'-end (useful when smallrna is sequenced). ========================= SAM/BAM related programs. They work with SAM/BAM input file(s). ns-bam2fastq Convert a SAM/BAM file into a FASTQ file. ns-bam-join Merge together two or more SAM/BAM files into one. ns-bam-split Split a SAM/BAM file into smaller fixed-length sets. ns-compute-profile Compute a coverage profile from a SAM/BAM file. The output can be in WIG or DCR format. ns-methylation-histograms Compute histograms for methylation contexts. ns-methylation-statistics Compute methylation-related statistics. ns-sam-filter Filter a SAM/BAM using mapping information. It can select uniquely/multiple mapped records, can work with paired-ends informations and it has many more filter. ns-sam-stats Compute alignment statistics for a SAM/BAM file. ======================= Miscellaneous programs. ns-csv-subset Given a comma separated file and a file with subset indication, extract/join informations for the subsets. ns-extract-from-wig Extract regions from a wig file. ns-random-subset Given a FASTA,/FASTQ (single-end or paired-ends), or a SAM/BAM file, extract a random subset. ... and many more ... ================ = INSTALLATION = ================ Before to install NGS-SUITE you need to download and install libbiocpp (http://libbiocpp.sf.net). Let $LIBBIOCPP_PATH (tipically somethink like "/usr/local/" or "/usr/local/libbiocpp/") just run: ./configure --with-libbiocpp=$LIBBIOCPP_PATH make make install That's all! Enjoy ngs-suite.