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- Jit@jit.aber
Jit created a new bio-script Convert fastq to fasta in Perl 2582 days ago
- Jit@jit.aber
Jit posted to the wire 2582 days ago

Bioinformatics blog http://onetipperday.sterding.com/ #Blog
- Rahul Agarwal@raag
Rahul Agarwal posted a new ad in the ResearchLabs Prof. Dr. rer. nat. Jeanette Erdmann's Lab 2582 days ago
- Jit@jit.aber
Jit created a new bio-script Loop over with all files in a directory in bash 2583 days ago
- Radha Agarkar@radhaagarkar
Radha Agarkar created a page Tools for bacterial whole genome annotation 2583 days ago

RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation...
- Jit@jit.aber
Jit posted to the wire 2583 days ago

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630013/ #Bacteria #NGS #Comparative #Genomics
- Rahul Agarwal@raag
Rahul Agarwal posted a new ad in the ResearchLabs Genomic approaches to study global regulation of gene expression in the mouse immune system 2584 days ago
- Robert M Willioms@robert
Robert M Willioms bookmarked SVfinder: Tool for detecting genomic rearrangement form DNA-seq data 2585 days ago

SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

https://github.com/cauyrd/SVfinder
- Jit@jit.aber
Jit created a new bio-script Clump Finding Problem Solved with Perl 2585 days ago
- Jit@jit.aber
Jit posted to the wire 2585 days ago

#Remove a #sequence by id from multifasta: cat vaga.fa | awk '{if (substr($0,1) == ">scaffold_1 1087316 bp") censor=1; else if (substr($0,1,1) == ">") censor=0; if (censor==0) print $0}' > fixed.fasta
- Jit@jit.aber
Jit posted to the wire 2586 days ago

awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} {if ($2) print ">"$0}' all_p_ctg.fa > all_p_ctg_CORRECTED.fa #remove #empty #clean #fasta
- Jit@jit.aber
Jit bookmarked TeachEnG: Teaching Engine for Genomics 2586 days ago

TeachEnG (pronounced “teaching”), a Teaching Engine for Genomics, provides educational games to help students and researchers understand key bioinformatics concepts. The current version includes interactive modules for sequence alignment...

http://teacheng.illinois.edu/
- Strand@Strand
Strand commented on the news Webinar on Unique Molecular Identifier (UMI)-powered Ultra-sensitive Variant Calling using Strand... 2587 days ago

Hurry! Limited seats available. To attend, register at http://www.strand-ngs.com/webinar_registration
- Jit@jit.aber
Jit bookmarked Mash: fast genome and metagenome distance estimation using MinHash 2587 days ago

Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is...

https://github.com/marbl/Mash/releases
- Jit@jit.aber
Jit bookmarked MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to... 2587 days ago

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...

https://github.com/marbl/MashMap
Comments
- Jit@jit.aber
  
  Jit 2374 days ago
  ➜ mashmap-Linux64-v2.0 git:(master) ✗ ./mashmap -h
  -----------------
  Mashmap is an approximate long read or contig mapper based on Jaccard
  similarity
  -----------------
  Example usage:
  $ mashmap -r ref.fa -q seq.fq [OPTIONS]
  $ mashmap --rl reference_files_list.txt -q seq.fq [OPTIONS]
  Available options
  -----------------
  -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@jit.aber
Jit commented on a bookmark List of Bioinformatics Vacancy, Jobs, Opportunity websites 2587 days ago

You can find bioinformatics jobs in RG https://www.researchgate.net/jobs
- Jit@jit.aber
Jit created a new bio-script Reformat the file names with Perl 2587 days ago
- Jit@jit.aber
Jit posted a new ad in the ResearchLabs Talkowski Laboratory 2588 days ago
- Neel@neelam
Neel bookmarked BBTools User Guide 2588 days ago

The guides describe the function, syntax, and typical use-cases of the tools; for a complete list of parameters, run the tool’s shellscript or open it with a text editor. Most tools do not currently have a guide, but each has shellscripts with...

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
- Poonam Mahapatra@poonam
Poonam Mahapatra posted to the wire 2588 days ago

Remove duplicate fasta ids: awk '/^>/{f=!d[$1];d[$1]=1}f' in.fa > out.fa #duplicate #fasta #ids

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