Now move to Github from https://sourceforge.net/projects/metabarcoding/.

Hao M, Jin Q, Meng G, Yang C, Yang S, Shi Z, Tang M, Liu S, Li Y, Li J, Zhang D. Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study. Evolutionary Ecology. 2020 Sep 5:1-26. DOI: https://doi.org/10.1007/s10682-020-10072-y

Can be found on https://sourceforge.net/projects/metabarcoding/.

Liu S, Li Y, Lu J, Su X, Tang M, Zhang R, Zhou L, Zhou C, Yang Q, Ji Y, Yu DW. SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods in Ecology and Evolution. 2013 Dec;4(12):1142-50. DOI: https://doi.org/10.1111/2041-210X.12120

version 4.6.8

modified by Guanliang Meng:

1. Fixed critical bugs on user-provided float assignment (wrongly used 'i' type instead of 'f' type in the GetOptions function).

version 4.6.7

modified by Guanliang Meng:

1. shorten the waiting interval time;
2. support multiple coverage and cluster thresholds by resuming running.

version 4.6

modified by Guanliang Meng:

1. add -view_opt option so that user can decide the prefect option for SAM file filtering during calculate site-depth.

version 4.5

modified by Guanliang Meng: 1) Fixed a bug in finding the barcodes from filenames in @flist and @slist; 2) Use SAM flag -F 3852 to replace -F 4 when filter SAM files.

Summary for SAM flag 3852: read unmapped (0x4); mate unmapped (0x8)*;
not primary alignment (0x100); read fails platform/vendor quality checks
(0x200); read is PCR or optical duplicate (0x400); supplementary
alignment (0x800);

*Warning: Flag(s) and 0x8 cannot be set when read is not paired

See https://broadinstitute.github.io/picard/explain-flags.html

version 4.4

modified by Guanliang Meng:

1. upgrade BWA '0.5.9-r16' to '0.7.17-r1198-dirty';

2. filter contigs with internal stop codons (translate 1,2,3 frames by default);

3. filter contigs with specific sequencing depth by mapping SLS against contigs.

Warning: The two new features DO NOT work for samples without barcode sequences ahead of the primers.

version 4.3

modified by Guanliang Meng:

1. use Parallel::ForkManager to deal with multi-samples at the same time;

2. support running tasks on localhost and SGE cluster;

3. support resumption of running tasks.

version 4.2

modified by Guanliang Meng:

1. use Log::Log4perl and Log::Dispatch for logging.

version 4.1

modified by Guanliang Meng:

1. add citation infor.

version 4.0

modified by Guanliang Meng:

1. change usearch to vsearch;

2. small bug fixed (partially) for reading a lib file (-lib option).

version 3.0

modified by Shanlin Liu:

1. protein express check can be skipped without setting -int and -pro n;

2. multiple primers with index ahead can be proccessed batching, however, if index exists at only one end of primers (e.g. former), it should be tackled one by one with parameter -len setted as 0;

3. PEAR was introduced as an option for shotgun reads overlap