Neel
Bioinformatics Beginner
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BBTools for bioinformatician !
By Surabhi Chaudhary 3155 days ago Comments (1)BBTools can do almost everything now !Alfred: BAM Statistics and Feature Counting
By Jit 3178 days agogear.embl.de - The easiest way to get Alfred is to download a statically linked binary from the Alfred github release page. Alternatively, you can build Alfred from source. Alfred dependencies are included as submodules so you need to do a recursive...mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 2518 days agogithub.com - mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...segemehl
By Anjana 3801 days agohoffmann.bioinf.uni-leipzig.de - segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is...WGS Celera Assembler version 8.3rc2
By Jit 3466 days agowgs-assembler.sourceforge.net - These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.This distribution package provides a stable, tested, documented version of the software. The distribution is usable on most Unix-like platforms,...Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 3249 days agogithub.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good...maftools : Summarize, Analyze and Visualize MAF Files
By Neel 2113 days agowww.bioconductor.org - With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widely accepted and used to store somatic variants detected. The Cancer Genome Atlas Project has sequenced over 30 different cancers with sample size of...“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
By Poonam Mahapatra 3046 days agodoua.prabi.fr - One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies,...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 3057 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit,...
By Neel 2433 days agowww.phrap.org - Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence...
